##fileformat=VCFv4.2
##fileDate=20210722
##source=freeBayes v1.3.2-dirty
##reference=/work/nikospech/SARS-CoV-2/ref/NC_045512.fasta
##contig=<ID=NC_045512.2,length=29903>
##phasing=none
##commandline="freebayes -f /work/nikospech/SARS-CoV-2/ref/NC_045512.fasta -F 0.01 -C 1 --pooled-continuous L23MM_S3_sorted_uniq.bam"
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
##SnpEffVersion="5.0 (build 2020-08-09 21:23), by Pablo Cingolani"
##SnpEffCmd="SnpEff  NC_045512.2 L23MM_S3_freebayes.vcf "
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected'">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
NC_045512.2	32	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=564;DPB=564;DPRA=0;EPP=3.0103;EPPR=12.7391;GTI=0;LEN=1;MEANALT=1;MQM=39;MQMR=15.4892;NS=1;NUMALT=1;ODDS=729.572;PAIRED=1;PAIREDR=0.362007;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=18462;RO=558;RPL=0;RPP=16.0391;RPPR=1214.69;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=304;SRP=12.7391;SRR=254;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-234C>A|||||234|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-234C>A|||||234|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-234C>A|||||234|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-234C>A|||||234|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-774C>A|||||774|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-774C>A|||||774|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2688C>A|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2688C>A|||||2688|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.32C>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:564:558,6:558:18462:6:204:0,-155.891,-622.102
NC_045512.2	64	.	CTC	TTT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X1M1X;DP=1151;DPB=1156;DPRA=0;EPP=4.08507;EPPR=7.37801;GTI=0;LEN=3;MEANALT=1;MQM=41.4444;MQMR=15.4496;NS=1;NUMALT=1;ODDS=740.69;PAIRED=1;PAIREDR=0.415399;PAO=15;PQA=262;PQR=0;PRO=0;QA=3503;QR=37047;RO=1052;RPL=6;RPP=169.029;RPPR=1164.09;RPR=93;RUN=1;SAF=53;SAP=4.08507;SAR=46;SRF=566;SRP=16.2208;SRR=486;TYPE=complex;ANN=TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-202_-200delCTCinsTTT|||||202|,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-202_-200delCTCinsTTT|||||202|WARNING_TRANSCRIPT_NO_STOP_CODON,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-202_-200delCTCinsTTT|||||202|WARNING_TRANSCRIPT_NO_STOP_CODON,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-202_-200delCTCinsTTT|||||202|,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-742_-740delCTCinsTTT|||||742|WARNING_TRANSCRIPT_NO_START_CODON,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-742_-740delCTCinsTTT|||||742|WARNING_TRANSCRIPT_NO_START_CODON,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2656_-2654delCTCinsTTT|||||2656|WARNING_TRANSCRIPT_NO_START_CODON,TTT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2656_-2654delCTCinsTTT|||||2656|WARNING_TRANSCRIPT_NO_START_CODON,TTT|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.64_66delCTCinsTTT||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1151:1052,99:1052:37047:99:3503:0,-95.224,-953.379
NC_045512.2	92	.	C	T	3142.56	.	AB=0.43932;ABP=16.1867;AC=1;AF=0.5;AN=2;AO=181;CIGAR=1X;DP=412;DPB=412;DPRA=0;EPP=3.11827;EPPR=3.47092;GTI=0;LEN=1;MEANALT=1;MQM=43.0718;MQMR=51.9048;NS=1;NUMALT=1;ODDS=723.602;PAIRED=0.933702;PAIREDR=0.982684;PAO=0;PQA=0;PQR=0;PRO=0;QA=6095;QR=8033;RO=231;RPL=38;RPP=135.278;RPPR=91.4578;RPR=143;RUN=1;SAF=92;SAP=3.11827;SAR=89;SRF=120;SRP=3.77173;SRR=111;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-174C>T|||||174|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-174C>T|||||174|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-174C>T|||||174|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-174C>T|||||174|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-714C>T|||||714|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-714C>T|||||714|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2628C>T|||||2628|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2628C>T|||||2628|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.92C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:412:231,181:231:8033:181:6095:-336.686,0,-565.664
NC_045512.2	100	.	C	T	3907.17	.	AB=0.441501;ABP=16.4753;AC=1;AF=0.5;AN=2;AO=200;CIGAR=1X;DP=453;DPB=453;DPRA=0;EPP=3.05373;EPPR=3.14817;GTI=0;LEN=1;MEANALT=2;MQM=45.335;MQMR=52.9603;NS=1;NUMALT=1;ODDS=899.659;PAIRED=0.935;PAIREDR=0.984127;PAO=0;PQA=0;PQR=0;PRO=0;QA=6978;QR=8772;RO=252;RPL=49;RPP=115.97;RPPR=69.74;RPR=151;RUN=1;SAF=102;SAP=3.18402;SAR=98;SRF=130;SRP=3.56179;SRR=122;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-166C>T|||||166|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-166C>T|||||166|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-166C>T|||||166|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-166C>T|||||166|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-706C>T|||||706|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-706C>T|||||706|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2620C>T|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2620C>T|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.100C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:453:252,200:252:8772:200:6978:-410.991,0,-630.697
NC_045512.2	124	.	G	A	1.09393E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=585;DPB=585;DPRA=0;EPP=4.09604;EPPR=6.62691;GTI=0;LEN=1;MEANALT=1;MQM=39.5;MQMR=50.1023;NS=1;NUMALT=1;ODDS=735.632;PAIRED=1;PAIREDR=0.968804;PAO=0;PQA=0;PQR=0;PRO=0;QA=266;QR=19810;RO=577;RPL=5;RPP=4.09604;RPPR=24.1793;RPR=3;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=296;SRP=3.85706;SRR=281;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-142G>A|||||142|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-142G>A|||||142|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-142G>A|||||142|WARNING_TRANSCRIPT_NO_STOP_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-142G>A|||||142|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-682G>A|||||682|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-682G>A|||||682|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2596G>A|||||2596|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2596G>A|||||2596|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.124G>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:585:577,8:577:19810:8:266:0,-157.006,-1656.16
NC_045512.2	164	.	C	T	6382.88	.	AB=0.480127;ABP=5.16796;AC=1;AF=0.5;AN=2;AO=302;CIGAR=1X;DP=629;DPB=629;DPRA=0;EPP=3.0103;EPPR=3.96948;GTI=0;LEN=1;MEANALT=2;MQM=45.1656;MQMR=52.0337;NS=1;NUMALT=1;ODDS=1469.71;PAIRED=0.960265;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=10610;QR=11356;RO=326;RPL=162;RPP=6.49041;RPPR=5.67468;RPR=140;RUN=1;SAF=153;SAP=3.12534;SAR=149;SRF=166;SRP=3.25009;SRR=160;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-102C>T|||||102|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-102C>T|||||102|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-102C>T|||||102|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-102C>T|||||102|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-642C>T|||||642|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-642C>T|||||642|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2556C>T|||||2556|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2556C>T|||||2556|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.164C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/1:629:326,302:326:11356:302:10610:-646.358,0,-794.471
NC_045512.2	210	.	G	T	14518.1	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=537;DPB=537;DPRA=0;EPP=3.0265;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=43.8228;MQMR=52;NS=1;NUMALT=1;ODDS=741.615;PAIRED=0.996269;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=18923;QR=14;RO=1;RPL=318;RPP=43.5228;RPPR=5.18177;RPR=218;RUN=1;SAF=265;SAP=3.15615;SAR=271;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-56G>T|||||56|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-56G>T|||||56|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-56G>T|||||56|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-56G>T|||||56|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-596G>T|||||596|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-596G>T|||||596|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2510G>T|||||2510|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2510G>T|||||2510|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.210G>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	1/1:537:1,536:1:14:536:18923:-1459.38,-160.253,0
NC_045512.2	241	.	C	T	12516.3	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=461;CIGAR=1X;DP=461;DPB=461;DPRA=0;EPP=3.12806;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=43.4707;MQMR=0;NS=1;NUMALT=1;ODDS=643.687;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=16150;QR=0;RO=0;RPL=224;RPP=3.80635;RPPR=0;RPR=237;RUN=1;SAF=232;SAP=3.05269;SAR=229;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.-25C>T|||||25|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.-25C>T|||||25|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.-25C>T|||||25|WARNING_TRANSCRIPT_NO_STOP_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.-25C>T|||||25|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2479C>T|||||2479|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2479C>T|||||2479|WARNING_TRANSCRIPT_NO_START_CODON,T|intergenic_region|MODIFIER|CHR_START-ORF1ab|CHR_START-GU280_gp01|intergenic_region|CHR_START-GU280_gp01|||n.241C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	1/1:461:0,461:0:0:461:16150:-1256.02,-138.775,0
NC_045512.2	280	.	CC	TT	3525.62	.	AB=0.387879;ABP=57.0602;AC=1;AF=0.5;AN=2;AO=192;CIGAR=2X;DP=495;DPB=497;DPRA=0;EPP=3.0103;EPPR=3.03906;GTI=0;LEN=2;MEANALT=2;MQM=42.0052;MQMR=49.4834;NS=1;NUMALT=1;ODDS=811.803;PAIRED=1;PAIREDR=0.993377;PAO=4;PQA=140;PQR=0;PRO=0;QA=6736;QR=10479;RO=302;RPL=98;RPP=3.19126;RPPR=3.72933;RPR=94;RUN=1;SAF=94;SAP=3.19126;SAR=98;SRF=148;SRP=3.26915;SRR=154;TYPE=mnp;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.15_16delCCinsTT|p.Pro6Ser|15/21291|15/21291|5/7096||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.15_16delCCinsTT|p.Pro6Ser|15/540|15/540|5/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.15_16delCCinsTT|p.Pro6Ser|15/540|15/540|5/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.15_16delCCinsTT|p.Pro6Ser|15/13218|15/13218|5/4405||,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-526_-525delCCinsTT|||||526|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-526_-525delCCinsTT|||||526|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2440_-2439delCCinsTT|||||2440|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2440_-2439delCCinsTT|||||2440|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:495:302,192:302:10479:192:6736:-365.116,0,-736.846
NC_045512.2	335	.	CGC	TGT	1775.99	.	AB=0.217114;ABP=547.262;AC=1;AF=0.5;AN=2;AO=170;CIGAR=1X1M1X;DP=783;DPB=785.333;DPRA=0;EPP=3.21467;EPPR=8.43363;GTI=0;LEN=3;MEANALT=4;MQM=46.1059;MQMR=51.1593;NS=1;NUMALT=1;ODDS=408.938;PAIRED=0.976471;PAIREDR=0.985222;PAO=7;PQA=223;PQR=0;PRO=0;QA=5931;QR=21070;RO=609;RPL=92;RPP=5.51388;RPPR=296.708;RPR=78;RUN=1;SAF=83;SAP=3.21467;SAR=87;SRF=319;SRP=6.009;SRR=290;TYPE=complex;ANN=TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.70_72delCGCinsTGT|p.Arg24Cys|70/21291|70/21291|24/7096||,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.70_72delCGCinsTGT|p.Arg24Cys|70/540|70/540|24/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.70_72delCGCinsTGT|p.Arg24Cys|70/540|70/540|24/179||WARNING_TRANSCRIPT_NO_STOP_CODON,TGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.70_72delCGCinsTGT|p.Arg24Cys|70/13218|70/13218|24/4405||,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-471_-469delCGCinsTGT|||||471|WARNING_TRANSCRIPT_NO_START_CODON,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-471_-469delCGCinsTGT|||||471|WARNING_TRANSCRIPT_NO_START_CODON,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2385_-2383delCGCinsTGT|||||2385|WARNING_TRANSCRIPT_NO_START_CODON,TGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2385_-2383delCGCinsTGT|||||2385|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:783:609,170:609:21070:170:5931:-241.995,0,-1561.83
NC_045512.2	346	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=914;DPB=914;DPRA=0;EPP=3.0103;EPPR=5.17216;GTI=0;LEN=1;MEANALT=1;MQM=47.6;MQMR=47.8728;NS=1;NUMALT=1;ODDS=1156.65;PAIRED=1;PAIREDR=0.915929;PAO=0;PQA=0;PQR=0;PRO=0;QA=347;QR=31647;RO=904;RPL=6;RPP=3.87889;RPPR=520.167;RPR=4;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=461;SRP=3.78857;SRR=443;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.81C>T|p.Leu27Leu|81/21291|81/21291|27/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.81C>T|p.Leu27Leu|81/540|81/540|27/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.81C>T|p.Leu27Leu|81/540|81/540|27/179||WARNING_TRANSCRIPT_NO_STOP_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.81C>T|p.Leu27Leu|81/13218|81/13218|27/4405||,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-460C>T|||||460|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-460C>T|||||460|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2374C>T|||||2374|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2374C>T|||||2374|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:914:904,10:904:31647:10:347:0,-246.309,-2560.77
NC_045512.2	396	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1364;DPB=1364;DPRA=0;EPP=3.12459;EPPR=4.1025;GTI=0;LEN=1;MEANALT=2;MQM=42.2632;MQMR=49.3222;NS=1;NUMALT=1;ODDS=1698.24;PAIRED=0.894737;PAIREDR=0.959821;PAO=0;PQA=0;PQR=0;PRO=0;QA=666;QR=46617;RO=1344;RPL=2;RPP=28.7251;RPPR=62.5707;RPR=17;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=677;SRP=3.17187;SRR=667;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.131A>G|p.Gln44Arg|131/21291|131/21291|44/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.131A>G|p.Gln44Arg|131/540|131/540|44/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.131A>G|p.Gln44Arg|131/540|131/540|44/179||WARNING_TRANSCRIPT_NO_STOP_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.131A>G|p.Gln44Arg|131/13218|131/13218|44/4405||,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-410A>G|||||410|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-410A>G|||||410|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2324A>G|||||2324|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2324A>G|||||2324|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1364:1344,19:1344:46617:19:666:0,-362.653,-3817.07
NC_045512.2	613	.	G	A	29424.0	.	AB=0.828234;ABP=1348.68;AC=1;AF=0.5;AN=2;AO=1191;CIGAR=1X;DP=1438;DPB=1438;DPRA=0;EPP=6.07516;EPPR=4.98836;GTI=0;LEN=1;MEANALT=1;MQM=50.6507;MQMR=52.753;NS=1;NUMALT=1;ODDS=354.736;PAIRED=0.991604;PAIREDR=0.991903;PAO=0;PQA=0;PQR=0;PRO=0;QA=41710;QR=8642;RO=247;RPL=553;RPP=16.1832;RPPR=4.07406;RPR=638;RUN=1;SAF=578;SAP=5.24376;SAR=613;SRF=120;SRP=3.44108;SRR=127;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.348G>A|p.Val116Val|348/21291|348/21291|116/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.348G>A|p.Val116Val|348/540|348/540|116/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.348G>A|p.Val116Val|348/540|348/540|116/179||WARNING_TRANSCRIPT_NO_STOP_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.348G>A|p.Val116Val|348/13218|348/13218|116/4405||,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-193G>A|||||193|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-193G>A|||||193|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2107G>A|||||2107|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2107G>A|||||2107|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1438:247,1191:247:8642:1191:41710:-3099.14,0,-308.276
NC_045512.2	682	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=79;CIGAR=1X;DP=1852;DPB=1852;DPRA=0;EPP=3.03779;EPPR=17.0482;GTI=0;LEN=1;MEANALT=3;MQM=38.1519;MQMR=50.3139;NS=1;NUMALT=1;ODDS=1840.13;PAIRED=0.949367;PAIREDR=0.967815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2754;QR=59839;RO=1771;RPL=4;RPP=141.572;RPPR=68.4377;RPR=75;RUN=1;SAF=39;SAP=3.03779;SAR=40;SRF=896;SRP=3.55102;SRR=875;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.417T>C|p.Asp139Asp|417/21291|417/21291|139/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/540|417/540|139/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/540|417/540|139/179||WARNING_TRANSCRIPT_NO_STOP_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.417T>C|p.Asp139Asp|417/13218|417/13218|139/4405||,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.-124T>C|||||124|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.-124T>C|||||124|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-2038T>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-2038T>C|||||2038|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1852:1771,79:1771:59839:79:2754:0,-360.966,-4800.3
NC_045512.2	823	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1547;DPB=1547;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=41.9545;MQMR=52.4665;NS=1;NUMALT=1;ODDS=1927.38;PAIRED=0.909091;PAIREDR=0.985564;PAO=0;PQA=0;PQR=0;PRO=0;QA=775;QR=52847;RO=1524;RPL=0;RPP=50.7827;RPPR=3.28957;RPR=22;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=753;SRP=3.47195;SRR=771;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.558C>T|p.Val186Val|558/21291|558/21291|186/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.558C>T|p.Val186Val|558/13218|558/13218|186/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.18C>T|p.Val6Val|18/1914|18/1914|6/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.18C>T|p.Val6Val|18/1914|18/1914|6/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1897C>T|||||1897|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1897C>T|||||1897|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*18C>T|||||18|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*18C>T|||||18|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1547:1524,22:1524:52847:22:775:0,-410.536,-4495.54
NC_045512.2	895	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=89;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0347;EPPR=3.70522;GTI=0;LEN=1;MEANALT=1;MQM=47.8876;MQMR=51.1881;NS=1;NUMALT=1;ODDS=1489.29;PAIRED=0.977528;PAIREDR=0.989716;PAO=0;PQA=0;PQR=0;PRO=0;QA=3176;QR=58126;RO=1653;RPL=47;RPP=3.62026;RPPR=3.11671;RPR=42;RUN=1;SAF=43;SAP=3.22989;SAR=46;SRF=800;SRP=6.70036;SRR=853;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.630A>T|p.Lys210Asn|630/21291|630/21291|210/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.630A>T|p.Lys210Asn|630/13218|630/13218|210/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.90A>T|p.Lys30Asn|90/1914|90/1914|30/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.90A>T|p.Lys30Asn|90/1914|90/1914|30/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1825A>T|||||1825|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1825A>T|||||1825|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*90A>T|||||90|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*90A>T|||||90|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1742:1653,89:1653:58126:89:3176:0,-268.331,-4688.37
NC_045512.2	913	.	C	T	353.303	.	AB=0.150661;ABP=1846.36;AC=1;AF=0.5;AN=2;AO=262;CIGAR=1X;DP=1739;DPB=1739;DPRA=0;EPP=3.04345;EPPR=3.93292;GTI=0;LEN=1;MEANALT=2;MQM=49.5611;MQMR=51.2447;NS=1;NUMALT=1;ODDS=81.351;PAIRED=1;PAIREDR=0.991842;PAO=0;PQA=0;PQR=0;PRO=0;QA=9234;QR=50659;RO=1471;RPL=143;RPP=7.78422;RPPR=8.5032;RPR=119;RUN=1;SAF=129;SAP=3.14291;SAR=133;SRF=719;SRP=4.61787;SRR=752;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.648C>T|p.Ser216Ser|648/21291|648/21291|216/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.648C>T|p.Ser216Ser|648/13218|648/13218|216/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.108C>T|p.Ser36Ser|108/1914|108/1914|36/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.108C>T|p.Ser36Ser|108/1914|108/1914|36/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1807C>T|||||1807|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1807C>T|||||1807|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*108C>T|||||108|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*108C>T|||||108|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1739:1471,262:1471:50659:262:9234:-245.319,0,-3801.26
NC_045512.2	1048	.	G	T	55959.4	.	AB=0.711473;ABP=1265.83;AC=1;AF=0.5;AN=2;AO=2313;CIGAR=1X;DP=3251;DPB=3251;DPRA=0;EPP=5.26439;EPPR=3.46404;GTI=0;LEN=1;MEANALT=1;MQM=49.3562;MQMR=51.451;NS=1;NUMALT=1;ODDS=3880.56;PAIRED=0.996541;PAIREDR=0.984009;PAO=0;PQA=0;PQR=0;PRO=0;QA=81232;QR=33087;RO=938;RPL=1050;RPP=45.6033;RPPR=91.9434;RPR=1263;RUN=1;SAF=1190;SAP=7.22463;SAR=1123;SRF=477;SRP=3.60294;SRR=461;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.783G>T|p.Lys261Asn|783/21291|783/21291|261/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.783G>T|p.Lys261Asn|783/13218|783/13218|261/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.243G>T|p.Lys81Asn|243/1914|243/1914|81/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.243G>T|p.Lys81Asn|243/1914|243/1914|81/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1672G>T|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1672G>T|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*243G>T|||||243|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*243G>T|||||243|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3251:938,2313:938:33087:2313:81232:-5740.35,0,-1833.27
NC_045512.2	1259	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=194;CIGAR=1X;DP=2654;DPB=2654;DPRA=0;EPP=3.05507;EPPR=3.26551;GTI=0;LEN=1;MEANALT=2;MQM=51.634;MQMR=51.1745;NS=1;NUMALT=1;ODDS=1663.73;PAIRED=1;PAIREDR=0.9939;PAO=0;PQA=0;PQR=0;PRO=0;QA=6829;QR=85866;RO=2459;RPL=120;RPP=26.695;RPPR=136.638;RPR=74;RUN=1;SAF=94;SAP=3.41325;SAR=100;SRF=1211;SRP=4.21922;SRR=1248;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.994C>T|p.Gln332*|994/21291|994/21291|332/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.994C>T|p.Gln332*|994/13218|994/13218|332/4405||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.454C>T|p.Gln152*|454/1914|454/1914|152/637||WARNING_TRANSCRIPT_NO_START_CODON,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.454C>T|p.Gln152*|454/1914|454/1914|152/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1461C>T|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1461C>T|||||1461|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*454C>T|||||454|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*454C>T|||||454|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2654:2459,194:2459:85866:194:6829:0,-215.703,-6715.49
NC_045512.2	1441	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1222;DPB=1222;DPRA=0;EPP=3.0103;EPPR=3.02655;GTI=0;LEN=1;MEANALT=2;MQM=53.5;MQMR=52.1155;NS=1;NUMALT=1;ODDS=1481.16;PAIRED=1;PAIREDR=0.978387;PAO=0;PQA=0;PQR=0;PRO=0;QA=644;QR=41870;RO=1203;RPL=12;RPP=7.35324;RPPR=9.29367;RPR=6;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=601;SRP=3.01211;SRR=602;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1176C>T|p.Gly392Gly|1176/21291|1176/21291|392/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1176C>T|p.Gly392Gly|1176/13218|1176/13218|392/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.636C>T|p.Gly212Gly|636/1914|636/1914|212/637||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.636C>T|p.Gly212Gly|636/1914|636/1914|212/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1279C>T|||||1279|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1279C>T|||||1279|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*636C>T|||||636|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*636C>T|||||636|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1222:1203,18:1203:41870:18:644:0,-310.787,-3538.8
NC_045512.2	1469	.	C	T	1.64659E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=109;CIGAR=1X;DP=1145;DPB=1145;DPRA=0;EPP=3.03022;EPPR=3.04384;GTI=0;LEN=1;MEANALT=1;MQM=44.6606;MQMR=52.5444;NS=1;NUMALT=1;ODDS=585.618;PAIRED=1;PAIREDR=0.985521;PAO=0;PQA=0;PQR=0;PRO=0;QA=3677;QR=36019;RO=1036;RPL=64;RPP=10.2021;RPPR=3.31213;RPR=45;RUN=1;SAF=54;SAP=3.03022;SAR=55;SRF=510;SRP=3.54688;SRR=526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1204C>T|p.Arg402Cys|1204/21291|1204/21291|402/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1204C>T|p.Arg402Cys|1204/13218|1204/13218|402/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.664C>T|p.Arg222Cys|664/1914|664/1914|222/637||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.664C>T|p.Arg222Cys|664/1914|664/1914|222/637||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1251C>T|||||1251|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1251C>T|||||1251|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*664C>T|||||664|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*664C>T|||||664|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1145:1036,109:1036:36019:109:3677:0,-58.5213,-2826.07
NC_045512.2	1485	.	GAG	GG	1184.03	.	AB=0.19145;ABP=892.781;AC=1;AF=0.5;AN=2;AO=206;CIGAR=1M1D1M;DP=1076;DPB=1009.33;DPRA=0;EPP=3.38978;EPPR=3.07291;GTI=0;LEN=1;MEANALT=4;MQM=47.3544;MQMR=51.9769;NS=1;NUMALT=1;ODDS=272.632;PAIRED=0.985437;PAIREDR=0.988466;PAO=3;PQA=102;PQR=102;PRO=3;QA=6730;QR=30243;RO=867;RPL=112;RPP=6.42563;RPPR=3.91445;RPR=94;RUN=1;SAF=100;SAP=3.38978;SAR=106;SRF=421;SRP=4.57566;SRR=446;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1221delA|p.Gly408fs|1221/21291|1221/21291|407/7096||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1221delA|p.Gly408fs|1221/13218|1221/13218|407/4405||,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.681delA|p.Gly228fs|681/1914|681/1914|227/637||WARNING_TRANSCRIPT_NO_START_CODON,GG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.681delA|p.Gly228fs|681/1914|681/1914|227/637||WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1234delA|||||1234|WARNING_TRANSCRIPT_NO_START_CODON,GG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1234delA|||||1234|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*681delA|||||681|WARNING_TRANSCRIPT_NO_STOP_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*681delA|||||681|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1076:867,206:867:30243:206:6730:-221.186,0,-2270.15
NC_045512.2	1644	.	ACAT	CCAA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X2M1X;DP=3724;DPB=3727;DPRA=0;EPP=3.0608;EPPR=4.80063;GTI=0;LEN=4;MEANALT=7;MQM=30.7209;MQMR=51.8566;NS=1;NUMALT=1;ODDS=4720.41;PAIRED=0.953488;PAIREDR=0.990461;PAO=12;PQA=304;PQR=0;PRO=0;QA=1484;QR=129421;RO=3669;RPL=20;RPP=3.46479;RPPR=579.566;RPR=23;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1875;SRP=6.89338;SRR=1794;TYPE=complex;ANN=CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1379_1382delACATinsCCAA|p.AsnIle460ThrAsn|1379/21291|1379/21291|460/7096||,CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1379_1382delACATinsCCAA|p.AsnIle460ThrAsn|1379/13218|1379/13218|460/4405||,CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.839_842delACATinsCCAA|p.AsnIle280ThrAsn|839/1914|839/1914|280/637||WARNING_TRANSCRIPT_NO_START_CODON,CCAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.839_842delACATinsCCAA|p.AsnIle280ThrAsn|839/1914|839/1914|280/637||WARNING_TRANSCRIPT_NO_START_CODON,CCAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1076_-1073delACATinsCCAA|||||1076|WARNING_TRANSCRIPT_NO_START_CODON,CCAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1076_-1073delACATinsCCAA|||||1076|WARNING_TRANSCRIPT_NO_START_CODON,CCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*839_*842delACATinsCCAA|||||839|WARNING_TRANSCRIPT_NO_STOP_CODON,CCAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*839_*842delACATinsCCAA|||||839|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3724:3669,43:3669:129421:43:1484:0,-1028.38,-11045.6
NC_045512.2	1656	.	TTGG	ATGT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X2M1X;DP=3885;DPB=3898;DPRA=0;EPP=3.0459;EPPR=10.286;GTI=0;LEN=4;MEANALT=8;MQM=32.3279;MQMR=51.9625;NS=1;NUMALT=1;ODDS=4763.18;PAIRED=0.934426;PAIREDR=0.988454;PAO=2;PQA=64;PQR=0;PRO=0;QA=2084;QR=133325;RO=3811;RPL=26;RPP=5.89373;RPPR=94.6332;RPR=35;RUN=1;SAF=32;SAP=3.33068;SAR=29;SRF=1958;SRP=9.29224;SRR=1853;TYPE=complex;ANN=ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1391_1394delTTGGinsATGT|p.ValGly464AspVal|1391/21291|1391/21291|464/7096||,ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1391_1394delTTGGinsATGT|p.ValGly464AspVal|1391/13218|1391/13218|464/4405||,ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.851_854delTTGGinsATGT|p.ValGly284AspVal|851/1914|851/1914|284/637||WARNING_TRANSCRIPT_NO_START_CODON,ATGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.851_854delTTGGinsATGT|p.ValGly284AspVal|851/1914|851/1914|284/637||WARNING_TRANSCRIPT_NO_START_CODON,ATGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1064_-1061delTTGGinsATGT|||||1064|WARNING_TRANSCRIPT_NO_START_CODON,ATGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1064_-1061delTTGGinsATGT|||||1064|WARNING_TRANSCRIPT_NO_START_CODON,ATGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*851_*854delTTGGinsATGT|||||851|WARNING_TRANSCRIPT_NO_STOP_CODON,ATGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*851_*854delTTGGinsATGT|||||851|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3885:3811,61:3811:133325:61:2084:0,-1032.69,-11349.3
NC_045512.2	1700	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=4549;DPB=4549;DPRA=0;EPP=3.53672;EPPR=3.26665;GTI=0;LEN=1;MEANALT=3;MQM=50.2121;MQMR=52.9005;NS=1;NUMALT=1;ODDS=5535.53;PAIRED=0.939394;PAIREDR=0.996653;PAO=0;PQA=0;PQR=0;PRO=0;QA=2243;QR=155182;RO=4481;RPL=36;RPP=4.19474;RPPR=3.01466;RPR=30;RUN=1;SAF=33;SAP=3.0103;SAR=33;SRF=2333;SRP=19.5956;SRR=2148;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1435T>C|p.Ser479Pro|1435/21291|1435/21291|479/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1435T>C|p.Ser479Pro|1435/13218|1435/13218|479/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.895T>C|p.Ser299Pro|895/1914|895/1914|299/637||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.895T>C|p.Ser299Pro|895/1914|895/1914|299/637||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-1020T>C|||||1020|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-1020T>C|||||1020|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*895T>C|||||895|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*895T>C|||||895|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4549:4481,66:4481:155182:66:2243:0,-1178.54,-13249.9
NC_045512.2	1820	.	G	A	1.28256E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=225;CIGAR=1X;DP=4790;DPB=4790;DPRA=0;EPP=3.25157;EPPR=5.0218;GTI=0;LEN=1;MEANALT=3;MQM=53.3333;MQMR=52.6884;NS=1;NUMALT=1;ODDS=4172.54;PAIRED=0.982222;PAIREDR=0.992326;PAO=0;PQA=0;PQR=0;PRO=0;QA=7870;QR=158733;RO=4561;RPL=134;RPP=20.855;RPPR=145.462;RPR=91;RUN=1;SAF=110;SAP=3.25157;SAR=115;SRF=2212;SRP=11.9461;SRR=2349;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1555G>A|p.Gly519Ser|1555/21291|1555/21291|519/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1555G>A|p.Gly519Ser|1555/13218|1555/13218|519/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1015G>A|p.Gly339Ser|1015/1914|1015/1914|339/637||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1015G>A|p.Gly339Ser|1015/1914|1015/1914|339/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-900G>A|||||900|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-900G>A|||||900|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1015G>A|||||1015|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1015G>A|||||1015|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4790:4561,225:4561:158733:225:7870:0,-756.291,-13041.7
NC_045512.2	2095	.	G	A	1.24765E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1292;DPB=1292;DPRA=0;EPP=3.0103;EPPR=3.50327;GTI=0;LEN=1;MEANALT=2;MQM=50;MQMR=50.7745;NS=1;NUMALT=1;ODDS=1604.84;PAIRED=1;PAIREDR=0.990573;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=43930;RO=1273;RPL=8;RPP=3.0103;RPPR=3.2167;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=636;SRP=3.01201;SRR=637;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1830G>A|p.Ser610Ser|1830/21291|1830/21291|610/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1830G>A|p.Ser610Ser|1830/13218|1830/13218|610/4405||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1290G>A|p.Ser430Ser|1290/1914|1290/1914|430/637||WARNING_TRANSCRIPT_NO_START_CODON,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1290G>A|p.Ser430Ser|1290/1914|1290/1914|430/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-625G>A|||||625|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-625G>A|||||625|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1290G>A|||||1290|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1290G>A|||||1290|WARNING_TRANSCRIPT_NO_STOP_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1292:1273,16:1273:43930:16:546:0,-341.229,-3662.66
NC_045512.2	2155	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1466;DPB=1466;DPRA=0;EPP=3.44459;EPPR=4.10732;GTI=0;LEN=1;MEANALT=3;MQM=42.65;MQMR=52.0596;NS=1;NUMALT=1;ODDS=1811.26;PAIRED=0.9;PAIREDR=0.991684;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=50315;RO=1443;RPL=11;RPP=3.44459;RPPR=55.6328;RPR=9;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=710;SRP=3.80636;SRR=733;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.1890G>A|p.Trp630*|1890/21291|1890/21291|630/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.1890G>A|p.Trp630*|1890/13218|1890/13218|630/4405||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding|1/1|c.1350G>A|p.Trp450*|1350/1914|1350/1914|450/637||WARNING_TRANSCRIPT_NO_START_CODON,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding|1/1|c.1350G>A|p.Trp450*|1350/1914|1350/1914|450/637||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.-565G>A|||||565|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.-565G>A|||||565|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1350G>A|||||1350|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1350G>A|||||1350|WARNING_TRANSCRIPT_NO_STOP_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1466:1443,20:1443:50315:20:708:0,-386.729,-4291.72
NC_045512.2	2763	.	TGC	TC	2885.41	.	AB=0.180095;ABP=2628.85;AC=1;AF=0.5;AN=2;AO=532;CIGAR=1M1D1M;DP=2954;DPB=2776.67;DPRA=0;EPP=3.15724;EPPR=4.17803;GTI=0;LEN=1;MEANALT=5;MQM=48.9643;MQMR=52.4178;NS=1;NUMALT=1;ODDS=664.391;PAIRED=0.99812;PAIREDR=0.992946;PAO=0;PQA=0;PQR=0;PRO=0;QA=17759;QR=83546;RO=2410;RPL=244;RPP=10.9125;RPPR=20.6704;RPR=288;RUN=1;SAF=261;SAP=3.41847;SAR=271;SRF=1192;SRP=3.61939;SRR=1218;TYPE=del;ANN=TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2499delG|p.Gln834fs|2499/21291|2499/21291|833/7096||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2499delG|p.Gln834fs|2499/13218|2499/13218|833/4405||,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.45delG|p.Gln16fs|45/5835|45/5835|15/1944||WARNING_TRANSCRIPT_NO_START_CODON,TC|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.45delG|p.Gln16fs|45/5835|45/5835|15/1944||WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*1959delG|||||1959|WARNING_TRANSCRIPT_NO_STOP_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*1959delG|||||1959|WARNING_TRANSCRIPT_NO_STOP_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*45delG|||||45|WARNING_TRANSCRIPT_NO_START_CODON,TC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*45delG|||||45|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2954:2410,532:2410:83546:532:17759:-579.218,0,-6324.54
NC_045512.2	3037	.	CTAC	TTAT,TTAC	50614.4	.	AB=0.158792,0.840721;ABP=2079.08,2073.16;AC=1,1;AF=0.5,0.5;AN=2;AO=326,1726;CIGAR=1X2M1X,1X3M;DP=2053;DPB=2097.75;DPRA=0,0;EPP=3.0103,3.03043;EPPR=0;GTI=0;LEN=4,1;MEANALT=3,3;MQM=46.1135,50.1877;MQMR=0;NS=1;NUMALT=2;ODDS=76.3459;PAIRED=1,0.998841;PAIREDR=0;PAO=96,83;PQA=2101.5,1661.5;PQR=0;PRO=0;QA=11160,56774;QR=0;RO=0;RPL=162,808;RPP=3.03694,18.2333;RPPR=0;RPR=164,918;RUN=1,1;SAF=165,869;SAP=3.11688,3.19147;SAR=161,857;SRF=0;SRP=0;SRR=0;TYPE=complex,snp;ANN=TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772C>T|p.Phe924Phe|2772/21291|2772/21291|924/7096||,TTAT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2772_2775delCTACinsTTAT|p.926|2772/21291|2772/21291|924/7096||,TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2772C>T|p.Phe924Phe|2772/13218|2772/13218|924/4405||,TTAT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2772_2775delCTACinsTTAT|p.926|2772/13218|2772/13218|924/4405||,TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,TTAT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.318_321delCTACinsTTAT|p.108|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,TTAC|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.318C>T|p.Phe106Phe|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,TTAT|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.318_321delCTACinsTTAT|p.108|318/5835|318/5835|106/1944||WARNING_TRANSCRIPT_NO_START_CODON,TTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,TTAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2232_*2235delCTACinsTTAT|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,TTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2232C>T|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,TTAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2232_*2235delCTACinsTTAT|||||2232|WARNING_TRANSCRIPT_NO_STOP_CODON,TTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON,TTAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*318_*321delCTACinsTTAT|||||318|WARNING_TRANSCRIPT_NO_START_CODON,TTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*318C>T|||||318|WARNING_TRANSCRIPT_NO_START_CODON,TTAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*318_*321delCTACinsTTAT|||||318|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/2:2053:0,326,1726:0:0:326,1726:11160,56774:-5303.39,-4514.98,-4416.84,-787.998,0,-268.42
NC_045512.2	3244	.	C	T	6.49718E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1X;DP=3062;DPB=3062;DPRA=0;EPP=3.0608;EPPR=6.84328;GTI=0;LEN=1;MEANALT=1;MQM=45.3721;MQMR=48.8029;NS=1;NUMALT=1;ODDS=3757.35;PAIRED=1;PAIREDR=0.991388;PAO=0;PQA=0;PQR=0;PRO=0;QA=1492;QR=106008;RO=3019;RPL=16;RPP=9.12072;RPPR=199.751;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1547;SRP=7.05619;SRR=1472;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.2979C>T|p.Gly993Gly|2979/21291|2979/21291|993/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.2979C>T|p.Gly993Gly|2979/13218|2979/13218|993/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.525C>T|p.Gly175Gly|525/5835|525/5835|175/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.525C>T|p.Gly175Gly|525/5835|525/5835|175/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2439C>T|||||2439|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2439C>T|||||2439|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*525C>T|||||525|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*525C>T|||||525|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3062:3019,43:3019:106008:43:1492:0,-801.627,-8549.01
NC_045512.2	3267	.	C	T	66510.3	.	AB=0.84347;ABP=3439.83;AC=1;AF=0.5;AN=2;AO=2829;CIGAR=1X;DP=3354;DPB=3354;DPRA=0;EPP=5.00677;EPPR=3.82253;GTI=0;LEN=1;MEANALT=2;MQM=48.4143;MQMR=52.4637;NS=1;NUMALT=1;ODDS=445.319;PAIRED=0.994344;PAIREDR=0.984733;PAO=0;PQA=0;PQR=0;PRO=0;QA=99448;QR=18506;RO=524;RPL=1337;RPP=21.4513;RPPR=8.99428;RPR=1492;RUN=1;SAF=1456;SAP=8.29813;SAR=1373;SRF=272;SRP=4.66791;SRR=252;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3002C>T|p.Thr1001Ile|3002/21291|3002/21291|1001/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3002C>T|p.Thr1001Ile|3002/13218|3002/13218|1001/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.548C>T|p.Thr183Ile|548/5835|548/5835|183/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.548C>T|p.Thr183Ile|548/5835|548/5835|183/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2462C>T|||||2462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2462C>T|||||2462|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*548C>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*548C>T|||||548|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3354:524,2829:524:18506:2829:99448:-7040.97,0,-580.514
NC_045512.2	3290	.	C	G	2.34573E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=92;CIGAR=1X;DP=3816;DPB=3816;DPRA=0;EPP=3.0103;EPPR=5.63136;GTI=0;LEN=1;MEANALT=3;MQM=39.1957;MQMR=50.4792;NS=1;NUMALT=1;ODDS=4359.88;PAIRED=0.978261;PAIREDR=0.986287;PAO=0;PQA=0;PQR=0;PRO=0;QA=3202;QR=130715;RO=3719;RPL=46;RPP=3.0103;RPPR=63.9266;RPR=46;RUN=1;SAF=46;SAP=3.0103;SAR=46;SRF=1908;SRP=8.50408;SRR=1811;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3025C>G|p.Gln1009Glu|3025/21291|3025/21291|1009/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3025C>G|p.Gln1009Glu|3025/13218|3025/13218|1009/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.571C>G|p.Gln191Glu|571/5835|571/5835|191/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.571C>G|p.Gln191Glu|571/5835|571/5835|191/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2485C>G|||||2485|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2485C>G|||||2485|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*571C>G|||||571|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*571C>G|||||571|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3816:3719,92:3719:130715:92:3202:0,-927.881,-10728.8
NC_045512.2	3327	.	AGA	AA	0.0	.	AB=0.133491;ABP=4451.89;AC=1;AF=0.5;AN=2;AO=509;CIGAR=1M1D1M;DP=3813;DPB=3645.33;DPRA=0;EPP=3.21934;EPPR=4.22957;GTI=0;LEN=1;MEANALT=5;MQM=51.2692;MQMR=52.2961;NS=1;NUMALT=1;ODDS=425.428;PAIRED=0.996071;PAIREDR=0.992104;PAO=2;PQA=68;PQR=102;PRO=3;QA=17227;QR=115481;RO=3293;RPL=269;RPP=6.59814;RPPR=7.55305;RPR=240;RUN=1;SAF=256;SAP=3.0487;SAR=253;SRF=1646;SRP=3.01096;SRR=1647;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3063delG|p.Thr1022fs|3063/21291|3063/21291|1021/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3063delG|p.Thr1022fs|3063/13218|3063/13218|1021/4405||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.609delG|p.Thr204fs|609/5835|609/5835|203/1944||WARNING_TRANSCRIPT_NO_START_CODON,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.609delG|p.Thr204fs|609/5835|609/5835|203/1944||WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2523delG|||||2523|WARNING_TRANSCRIPT_NO_STOP_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2523delG|||||2523|WARNING_TRANSCRIPT_NO_STOP_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*609delG|||||609|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*609delG|||||609|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3813:3293,509:3293:115481:509:17227:-318.157,0,-8788
NC_045512.2	3483	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2793;DPB=2793;DPRA=0;EPP=3.07234;EPPR=8.70913;GTI=0;LEN=1;MEANALT=3;MQM=39.1143;MQMR=51.0527;NS=1;NUMALT=1;ODDS=3506.37;PAIRED=0.885714;PAIREDR=0.984381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1145;QR=96319;RO=2753;RPL=7;RPP=30.3709;RPPR=550.326;RPR=28;RUN=1;SAF=16;SAP=3.56868;SAR=19;SRF=1344;SRP=6.34284;SRR=1409;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3218G>T|p.Gly1073Val|3218/21291|3218/21291|1073/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3218G>T|p.Gly1073Val|3218/13218|3218/13218|1073/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.764G>T|p.Gly255Val|764/5835|764/5835|255/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.764G>T|p.Gly255Val|764/5835|764/5835|255/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2678G>T|||||2678|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2678G>T|||||2678|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*764G>T|||||764|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*764G>T|||||764|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2793:2753,35:2753:96319:35:1145:0,-756.489,-8079.93
NC_045512.2	3491	.	AA	TT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=2X;DP=2589;DPB=2589;DPRA=0;EPP=3.0565;EPPR=13.3547;GTI=0;LEN=2;MEANALT=3;MQM=40;MQMR=50.6949;NS=1;NUMALT=1;ODDS=3087.91;PAIRED=0.914894;PAIREDR=0.983858;PAO=0;PQA=0;PQR=0;PRO=0;QA=1679;QR=89098;RO=2540;RPL=16;RPP=13.4056;RPPR=539.265;RPR=31;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1223;SRP=10.5643;SRR=1317;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3226_3227delAAinsTT|p.Asn1076Phe|3226/21291|3226/21291|1076/7096||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3226_3227delAAinsTT|p.Asn1076Phe|3226/13218|3226/13218|1076/4405||,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.772_773delAAinsTT|p.Asn258Phe|772/5835|772/5835|258/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.772_773delAAinsTT|p.Asn258Phe|772/5835|772/5835|258/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2686_*2687delAAinsTT|||||2686|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2686_*2687delAAinsTT|||||2686|WARNING_TRANSCRIPT_NO_STOP_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*772_*773delAAinsTT|||||772|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*772_*773delAAinsTT|||||772|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2589:2540,47:2540:89098:47:1679:0,-657.215,-7396.86
NC_045512.2	3500	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2368;DPB=2368;DPRA=0;EPP=3.40914;EPPR=11.1091;GTI=0;LEN=1;MEANALT=1;MQM=47.1429;MQMR=50.5442;NS=1;NUMALT=1;ODDS=2753.48;PAIRED=0.918367;PAIREDR=0.983614;PAO=0;PQA=0;PQR=0;PRO=0;QA=1649;QR=80645;RO=2319;RPL=15;RPP=19.0083;RPPR=387.752;RPR=34;RUN=1;SAF=25;SAP=3.05462;SAR=24;SRF=1130;SRP=6.26985;SRR=1189;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3235A>C|p.Thr1079Pro|3235/21291|3235/21291|1079/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3235A>C|p.Thr1079Pro|3235/13218|3235/13218|1079/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.781A>C|p.Thr261Pro|781/5835|781/5835|261/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.781A>C|p.Thr261Pro|781/5835|781/5835|261/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2695A>C|||||2695|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2695A>C|||||2695|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*781A>C|||||781|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*781A>C|||||781|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2368:2319,49:2319:80645:49:1649:0,-578.836,-6661.83
NC_045512.2	3522	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=156;CIGAR=1X;DP=1893;DPB=1893;DPRA=0;EPP=3.51141;EPPR=16.793;GTI=0;LEN=1;MEANALT=1;MQM=49.0577;MQMR=51.5181;NS=1;NUMALT=1;ODDS=1071.28;PAIRED=0.961538;PAIREDR=0.98388;PAO=0;PQA=0;PQR=0;PRO=0;QA=5381;QR=60781;RO=1737;RPL=55;RPP=32.4644;RPPR=275.649;RPR=101;RUN=1;SAF=76;SAP=3.23302;SAR=80;SRF=845;SRP=5.77183;SRR=892;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3257A>T|p.Glu1086Val|3257/21291|3257/21291|1086/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3257A>T|p.Glu1086Val|3257/13218|3257/13218|1086/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.803A>T|p.Glu268Val|803/5835|803/5835|268/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.803A>T|p.Glu268Val|803/5835|803/5835|268/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2717A>T|||||2717|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2717A>T|||||2717|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*803A>T|||||803|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*803A>T|||||803|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1893:1737,156:1737:60781:156:5381:0,-119.28,-4729.35
NC_045512.2	3668	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1674;DPB=1674;DPRA=0;EPP=3.13803;EPPR=3.76559;GTI=0;LEN=1;MEANALT=2;MQM=42.4118;MQMR=52.933;NS=1;NUMALT=1;ODDS=2143.47;PAIRED=0.882353;PAIREDR=0.9843;PAO=0;PQA=0;PQR=0;PRO=0;QA=572;QR=58169;RO=1656;RPL=11;RPP=6.20364;RPPR=3.19912;RPR=6;RUN=1;SAF=10;SAP=4.1599;SAR=7;SRF=834;SRP=3.19912;SRR=822;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3403T>G|p.Tyr1135Asp|3403/21291|3403/21291|1135/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3403T>G|p.Tyr1135Asp|3403/13218|3403/13218|1135/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.949T>G|p.Tyr317Asp|949/5835|949/5835|317/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.949T>G|p.Tyr317Asp|949/5835|949/5835|317/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4887T>G|||||4887|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4887T>G|||||4887|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*2863T>G|||||2863|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*2863T>G|||||2863|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*949T>G|||||949|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*949T>G|||||949|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1674:1656,17:1656:58169:17:572:0,-462.9,-5012.95
NC_045512.2	3961	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=1X;DP=455;DPB=455;DPRA=0;EPP=3.44459;EPPR=3.0296;GTI=0;LEN=1;MEANALT=1;MQM=55.2;MQMR=53.5956;NS=1;NUMALT=1;ODDS=575.059;PAIRED=1;PAIREDR=0.991111;PAO=0;PQA=0;PQR=0;PRO=0;QA=180;QR=15627;RO=450;RPL=2;RPP=3.44459;RPPR=3.0103;RPR=3;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=227;SRP=3.08751;SRR=223;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3696C>T|p.Ile1232Ile|3696/21291|3696/21291|1232/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3696C>T|p.Ile1232Ile|3696/13218|3696/13218|1232/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1242C>T|p.Ile414Ile|1242/5835|1242/5835|414/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1242C>T|p.Ile414Ile|1242/5835|1242/5835|414/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4594C>T|||||4594|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4594C>T|||||4594|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3156C>T|||||3156|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3156C>T|||||3156|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1242C>T|||||1242|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1242C>T|||||1242|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:455:450,5:450:15627:5:180:0,-120.462,-1356.23
NC_045512.2	4038	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=363;DPB=363;DPRA=0;EPP=3.0103;EPPR=3.30835;GTI=0;LEN=1;MEANALT=1;MQM=37.8333;MQMR=54.3165;NS=1;NUMALT=1;ODDS=446.545;PAIRED=1;PAIREDR=0.994398;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=12513;RO=357;RPL=6;RPP=16.0391;RPPR=22.7725;RPR=0;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=176;SRP=3.16236;SRR=181;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3773A>C|p.Asp1258Ala|3773/21291|3773/21291|1258/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3773A>C|p.Asp1258Ala|3773/13218|3773/13218|1258/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1319A>C|p.Asp440Ala|1319/5835|1319/5835|440/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1319A>C|p.Asp440Ala|1319/5835|1319/5835|440/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4517A>C|||||4517|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4517A>C|||||4517|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3233A>C|||||3233|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3233A>C|||||3233|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1319A>C|||||1319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1319A>C|||||1319|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:363:357,6:357:12513:6:216:0,-92.3258,-1088.77
NC_045512.2	4102	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1952;DPB=1952;DPRA=0;EPP=3.0103;EPPR=4.46694;GTI=0;LEN=1;MEANALT=1;MQM=38.85;MQMR=51.4073;NS=1;NUMALT=1;ODDS=2496.52;PAIRED=1;PAIREDR=0.98913;PAO=0;PQA=0;PQR=0;PRO=0;QA=708;QR=67459;RO=1932;RPL=4;RPP=18.6449;RPPR=1095.71;RPR=16;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=983;SRP=4.30959;SRR=949;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3837A>T|p.Leu1279Phe|3837/21291|3837/21291|1279/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3837A>T|p.Leu1279Phe|3837/13218|3837/13218|1279/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1383A>T|p.Leu461Phe|1383/5835|1383/5835|461/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1383A>T|p.Leu461Phe|1383/5835|1383/5835|461/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4453A>T|||||4453|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4453A>T|||||4453|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3297A>T|||||3297|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3297A>T|||||3297|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1383A>T|||||1383|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1383A>T|||||1383|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1952:1932,20:1932:67459:20:708:0,-538.151,-5712.79
NC_045512.2	4162	.	G	T	3.59212E-13	.	AB=0.123522;ABP=2813.62;AC=1;AF=0.5;AN=2;AO=282;CIGAR=1X;DP=2283;DPB=2283;DPRA=0;EPP=3.0411;EPPR=5.40749;GTI=0;LEN=1;MEANALT=1;MQM=49.4752;MQMR=50.932;NS=1;NUMALT=1;ODDS=430.424;PAIRED=0.98227;PAIREDR=0.996002;PAO=0;PQA=0;PQR=0;PRO=0;QA=9779;QR=69865;RO=2001;RPL=137;RPP=3.50312;RPPR=113.441;RPR=145;RUN=1;SAF=145;SAP=3.50312;SAR=137;SRF=1019;SRP=4.49593;SRR=982;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3897G>T|p.Val1299Val|3897/21291|3897/21291|1299/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3897G>T|p.Val1299Val|3897/13218|3897/13218|1299/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1443G>T|p.Val481Val|1443/5835|1443/5835|481/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1443G>T|p.Val481Val|1443/5835|1443/5835|481/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4393G>T|||||4393|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4393G>T|||||4393|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3357G>T|||||3357|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3357G>T|||||3357|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1443G>T|||||1443|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1443G>T|||||1443|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2283:2001,282:2001:69865:282:9779:-137.285,0,-5222.59
NC_045512.2	4181	.	G	T	28777.7	.	AB=0.575386;ABP=111.706;AC=1;AF=0.5;AN=2;AO=1267;CIGAR=1X;DP=2202;DPB=2202;DPRA=0;EPP=4.08147;EPPR=3.24279;GTI=0;LEN=1;MEANALT=2;MQM=48.9811;MQMR=52.2934;NS=1;NUMALT=1;ODDS=4866.93;PAIRED=0.998421;PAIREDR=0.995717;PAO=0;PQA=0;PQR=0;PRO=0;QA=43524;QR=32368;RO=934;RPL=667;RPP=10.7039;RPPR=3.15909;RPR=600;RUN=1;SAF=646;SAP=4.08147;SAR=621;SRF=479;SRP=4.34945;SRR=455;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.3916G>T|p.Ala1306Ser|3916/21291|3916/21291|1306/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.3916G>T|p.Ala1306Ser|3916/13218|3916/13218|1306/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1462G>T|p.Ala488Ser|1462/5835|1462/5835|488/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1462G>T|p.Ala488Ser|1462/5835|1462/5835|488/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4374G>T|||||4374|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4374G>T|||||4374|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3376G>T|||||3376|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3376G>T|||||3376|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1462G>T|||||1462|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1462G>T|||||1462|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2202:934,1267:934:32368:1267:43524:-2898.44,0,-2133.35
NC_045512.2	4268	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.0103;EPPR=3.01402;GTI=0;LEN=1;MEANALT=1;MQM=37.5312;MQMR=52.0746;NS=1;NUMALT=1;ODDS=2958.12;PAIRED=0.5625;PAIREDR=0.985849;PAO=0;PQA=0;PQR=0;PRO=0;QA=1148;QR=82280;RO=2332;RPL=31;RPP=64.083;RPPR=3.0103;RPR=1;RUN=1;SAF=15;SAP=3.28173;SAR=17;SRF=1169;SRP=3.04382;SRR=1163;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4003A>G|p.Asn1335Asp|4003/21291|4003/21291|1335/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4003A>G|p.Asn1335Asp|4003/13218|4003/13218|1335/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1549A>G|p.Asn517Asp|1549/5835|1549/5835|517/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1549A>G|p.Asn517Asp|1549/5835|1549/5835|517/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4287A>G|||||4287|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4287A>G|||||4287|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3463A>G|||||3463|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3463A>G|||||3463|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1549A>G|||||1549|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1549A>G|||||1549|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2364:2332,32:2332:82280:32:1148:0,-633.643,-7000.81
NC_045512.2	4435	.	T	C	3.44749E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=25;CIGAR=1X;DP=1857;DPB=1857;DPRA=0;EPP=3.79203;EPPR=7.42322;GTI=0;LEN=1;MEANALT=2;MQM=57.28;MQMR=53.1436;NS=1;NUMALT=1;ODDS=2286.49;PAIRED=1;PAIREDR=0.995085;PAO=0;PQA=0;PQR=0;PRO=0;QA=807;QR=64472;RO=1831;RPL=10;RPP=5.18177;RPPR=3.63767;RPR=15;RUN=1;SAF=13;SAP=3.09716;SAR=12;SRF=931;SRP=4.15;SRR=900;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4170T>C|p.Pro1390Pro|4170/21291|4170/21291|1390/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4170T>C|p.Pro1390Pro|4170/13218|4170/13218|1390/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.1716T>C|p.Pro572Pro|1716/5835|1716/5835|572/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.1716T>C|p.Pro572Pro|1716/5835|1716/5835|572/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-4120T>C|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-4120T>C|||||4120|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3630T>C|||||3630|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3630T>C|||||3630|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*1716T>C|||||1716|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*1716T>C|||||1716|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1857:1831,25:1831:64472:25:807:0,-486.055,-5542.5
NC_045512.2	4747	.	T	C	8.73969E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=644;DPB=644;DPRA=0;EPP=3.55317;EPPR=3.59559;GTI=0;LEN=1;MEANALT=2;MQM=41.0625;MQMR=53.3876;NS=1;NUMALT=1;ODDS=745.803;PAIRED=0.625;PAIREDR=0.985646;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=21917;RO=627;RPL=0;RPP=37.7539;RPPR=23.544;RPR=16;RUN=1;SAF=7;SAP=3.55317;SAR=9;SRF=326;SRP=5.17485;SRR=301;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4482T>C|p.Ser1494Ser|4482/21291|4482/21291|1494/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4482T>C|p.Ser1494Ser|4482/13218|4482/13218|1494/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2028T>C|p.Ser676Ser|2028/5835|2028/5835|676/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2028T>C|p.Ser676Ser|2028/5835|2028/5835|676/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3808T>C|||||3808|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3808T>C|||||3808|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3942T>C|||||3942|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3942T>C|||||3942|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2028T>C|||||2028|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2028T>C|||||2028|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:644:627,16:627:21917:16:576:0,-153.532,-1879.62
NC_045512.2	4752	.	C	T	2.15769E-13	.	AB=0.138414;ABP=733.223;AC=1;AF=0.5;AN=2;AO=89;CIGAR=1X;DP=643;DPB=643;DPRA=0;EPP=3.22989;EPPR=3.67391;GTI=0;LEN=1;MEANALT=2;MQM=48.8427;MQMR=53.2984;NS=1;NUMALT=1;ODDS=48.6552;PAIRED=0.977528;PAIREDR=0.976492;PAO=0;PQA=0;PQR=0;PRO=0;QA=3118;QR=19372;RO=553;RPL=48;RPP=4.20583;RPPR=10.9619;RPR=41;RUN=1;SAF=45;SAP=3.0347;SAR=44;SRF=279;SRP=3.10847;SRR=274;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4487C>T|p.Thr1496Ile|4487/21291|4487/21291|1496/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4487C>T|p.Thr1496Ile|4487/13218|4487/13218|1496/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2033C>T|p.Thr678Ile|2033/5835|2033/5835|678/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2033C>T|p.Thr678Ile|2033/5835|2033/5835|678/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3803C>T|||||3803|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3803C>T|||||3803|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*3947C>T|||||3947|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*3947C>T|||||3947|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2033C>T|||||2033|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2033C>T|||||2033|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:643:553,89:553:19372:89:3118:-66.622,0,-1499.26
NC_045512.2	4839	.	T	C	1.23554E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=596;DPB=596;DPRA=0;EPP=3.0103;EPPR=3.02502;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.1797;NS=1;NUMALT=1;ODDS=758.227;PAIRED=1;PAIREDR=0.99322;PAO=0;PQA=0;PQR=0;PRO=0;QA=212;QR=20811;RO=590;RPL=2;RPP=4.45795;RPPR=5.49829;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=298;SRP=3.1428;SRR=292;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4574T>C|p.Ile1525Thr|4574/21291|4574/21291|1525/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4574T>C|p.Ile1525Thr|4574/13218|4574/13218|1525/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2120T>C|p.Ile707Thr|2120/5835|2120/5835|707/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2120T>C|p.Ile707Thr|2120/5835|2120/5835|707/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3716T>C|||||3716|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3716T>C|||||3716|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4034T>C|||||4034|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4034T>C|||||4034|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2120T>C|||||2120|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2120T>C|||||2120|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:596:590,6:590:20811:6:212:0,-160.023,-1801.04
NC_045512.2	4850	.	A	G	8.74157E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=8;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.0103;EPPR=3.06442;GTI=0;LEN=1;MEANALT=1;MQM=40.625;MQMR=53.7212;NS=1;NUMALT=1;ODDS=823.193;PAIRED=1;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=284;QR=22334;RO=642;RPL=0;RPP=20.3821;RPPR=3.0103;RPR=8;RUN=1;SAF=4;SAP=3.0103;SAR=4;SRF=320;SRP=3.02383;SRR=322;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4585A>G|p.Lys1529Glu|4585/21291|4585/21291|1529/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4585A>G|p.Lys1529Glu|4585/13218|4585/13218|1529/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2131A>G|p.Lys711Glu|2131/5835|2131/5835|711/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2131A>G|p.Lys711Glu|2131/5835|2131/5835|711/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3705A>G|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3705A>G|||||3705|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4045A>G|||||4045|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4045A>G|||||4045|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2131A>G|||||2131|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2131A>G|||||2131|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:650:642,8:642:22334:8:284:0,-174.183,-1944
NC_045512.2	4955	.	GAAGT	GAGT,GACGT	2.43493E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,48;CIGAR=1M1D3M,2M1X2M;DP=1155;DPB=1152;DPRA=0,0;EPP=3.17734,3.0103;EPPR=4.68418;GTI=0;LEN=1,1;MEANALT=4,4;MQM=43.8462,51.9167;MQMR=50.1815;NS=1;NUMALT=2;ODDS=1052.3;PAIRED=1,1;PAIREDR=0.983501;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,1680;QR=38285;RO=1091;RPL=0,32;RPP=31.2394,14.5915;RPPR=594.194;RPR=13,16;RUN=1,1;SAF=7,24;SAP=3.17734,3.0103;SAR=6,24;SRF=549;SRP=3.10783;SRR=542;TYPE=del,snp;ANN=GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4692delA|p.Val1565fs|4692/21291|4692/21291|1564/7096||,GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4692delA|p.Val1565fs|4692/13218|4692/13218|1564/4405||,GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2238delA|p.Val747fs|2238/5835|2238/5835|746/1944||WARNING_TRANSCRIPT_NO_START_CODON,GAGT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2238delA|p.Val747fs|2238/5835|2238/5835|746/1944||WARNING_TRANSCRIPT_NO_START_CODON,GACGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4692A>C|p.Glu1564Asp|4692/21291|4692/21291|1564/7096||,GACGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4692A>C|p.Glu1564Asp|4692/13218|4692/13218|1564/4405||,GACGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2238A>C|p.Glu746Asp|2238/5835|2238/5835|746/1944||WARNING_TRANSCRIPT_NO_START_CODON,GACGT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2238A>C|p.Glu746Asp|2238/5835|2238/5835|746/1944||WARNING_TRANSCRIPT_NO_START_CODON,GAGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3598delA|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,GACGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3598A>C|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,GAGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3598delA|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,GACGT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3598A>C|||||3598|WARNING_TRANSCRIPT_NO_START_CODON,GAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4152delA|||||4152|WARNING_TRANSCRIPT_NO_STOP_CODON,GACGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4152A>C|||||4152|WARNING_TRANSCRIPT_NO_STOP_CODON,GAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4152delA|||||4152|WARNING_TRANSCRIPT_NO_STOP_CODON,GACGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4152A>C|||||4152|WARNING_TRANSCRIPT_NO_STOP_CODON,GAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2238delA|||||2238|WARNING_TRANSCRIPT_NO_START_CODON,GACGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2238A>C|||||2238|WARNING_TRANSCRIPT_NO_START_CODON,GAGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2238delA|||||2238|WARNING_TRANSCRIPT_NO_START_CODON,GACGT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2238A>C|||||2238|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1155:1091,13,48:1091:38285:13,48:392,1680:0,-298.202,-3197.09,-193.338,-3065.95,-3081.74
NC_045512.2	5118	.	TTT	AAA	7.71464E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=3X;DP=2311;DPB=2311;DPRA=0;EPP=5.48477;EPPR=3.51746;GTI=0;LEN=3;MEANALT=3;MQM=46.9535;MQMR=53.1435;NS=1;NUMALT=1;ODDS=2722.45;PAIRED=1;PAIREDR=0.996026;PAO=0;PQA=0;PQR=0;PRO=0;QA=1544;QR=79153;RO=2265;RPL=16;RPP=9.12072;RPPR=37.9849;RPR=27;RUN=1;SAF=23;SAP=3.46479;SAR=20;SRF=1141;SRP=3.28737;SRR=1124;TYPE=complex;ANN=AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4853_4855delTTTinsAAA|p.PheTyr1618*|4853/21291|4853/21291|1618/7096||,AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4853_4855delTTTinsAAA|p.PheTyr1618*|4853/13218|4853/13218|1618/4405||,AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2399_2401delTTTinsAAA|p.PheTyr800*|2399/5835|2399/5835|800/1944||WARNING_TRANSCRIPT_NO_START_CODON,AAA|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2399_2401delTTTinsAAA|p.PheTyr800*|2399/5835|2399/5835|800/1944||WARNING_TRANSCRIPT_NO_START_CODON,AAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3437_-3435delTTTinsAAA|||||3437|WARNING_TRANSCRIPT_NO_START_CODON,AAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3437_-3435delTTTinsAAA|||||3437|WARNING_TRANSCRIPT_NO_START_CODON,AAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4937_-4935delTTTinsAAA|||||4937|WARNING_TRANSCRIPT_NO_START_CODON,AAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4937_-4935delTTTinsAAA|||||4937|WARNING_TRANSCRIPT_NO_START_CODON,AAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4313_*4315delTTTinsAAA|||||4313|WARNING_TRANSCRIPT_NO_STOP_CODON,AAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4313_*4315delTTTinsAAA|||||4313|WARNING_TRANSCRIPT_NO_STOP_CODON,AAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2399_*2401delTTTinsAAA|||||2399|WARNING_TRANSCRIPT_NO_START_CODON,AAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2399_*2401delTTTinsAAA|||||2399|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.04);NMD=(ORF1ab|GU280_gp01|28|0.04)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2311:2265,43:2265:79153:43:1544:0,-573.594,-6798.82
NC_045512.2	5182	.	T	C	7092.28	.	AB=0.252637;ABP=1061.18;AC=1;AF=0.5;AN=2;AO=503;CIGAR=1X;DP=1991;DPB=1991;DPRA=0;EPP=3.53266;EPPR=4.15595;GTI=0;LEN=1;MEANALT=3;MQM=48.9344;MQMR=52.5188;NS=1;NUMALT=1;ODDS=1633.06;PAIRED=0.986083;PAIREDR=0.992598;PAO=0;PQA=0;PQR=0;PRO=0;QA=17356;QR=52385;RO=1486;RPL=246;RPP=3.53266;RPPR=4.50666;RPR=257;RUN=1;SAF=250;SAP=3.04915;SAR=253;SRF=734;SRP=3.48376;SRR=752;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4917T>C|p.Asp1639Asp|4917/21291|4917/21291|1639/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4917T>C|p.Asp1639Asp|4917/13218|4917/13218|1639/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2463T>C|p.Asp821Asp|2463/5835|2463/5835|821/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2463T>C|p.Asp821Asp|2463/5835|2463/5835|821/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3373T>C|||||3373|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3373T>C|||||3373|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4873T>C|||||4873|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4873T>C|||||4873|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4377T>C|||||4377|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4377T>C|||||4377|WARNING_TRANSCRIPT_NO_STOP_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2463T>C|||||2463|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2463T>C|||||2463|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1991:1486,503:1486:52385:503:17356:-827.643,0,-3932.59
NC_045512.2	5184	.	C	T	1768.41	.	AB=0.166249;ABP=1935.14;AC=1;AF=0.5;AN=2;AO=332;CIGAR=1X;DP=1997;DPB=1997;DPRA=0;EPP=3.03646;EPPR=3.82738;GTI=0;LEN=1;MEANALT=2;MQM=50.6807;MQMR=51.7821;NS=1;NUMALT=1;ODDS=407.191;PAIRED=1;PAIREDR=0.989163;PAO=0;PQA=0;PQR=0;PRO=0;QA=11718;QR=57567;RO=1661;RPL=186;RPP=13.4752;RPPR=3.16849;RPR=146;RUN=1;SAF=167;SAP=3.03646;SAR=165;SRF=823;SRP=3.30445;SRR=838;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4919C>T|p.Pro1640Leu|4919/21291|4919/21291|1640/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4919C>T|p.Pro1640Leu|4919/13218|4919/13218|1640/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2465C>T|p.Pro822Leu|2465/5835|2465/5835|822/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2465C>T|p.Pro822Leu|2465/5835|2465/5835|822/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3371C>T|||||3371|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3371C>T|||||3371|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4871C>T|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4871C>T|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4379C>T|||||4379|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4379C>T|||||4379|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2465C>T|||||2465|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2465C>T|||||2465|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1997:1661,332:1661:57567:332:11718:-395.676,0,-4326.74
NC_045512.2	5239	.	C	T	8067.02	.	AB=0.283776;ABP=721.382;AC=1;AF=0.5;AN=2;AO=502;CIGAR=1X;DP=1769;DPB=1769;DPRA=0;EPP=3.63319;EPPR=4.45394;GTI=0;LEN=1;MEANALT=2;MQM=46.5538;MQMR=52.3399;NS=1;NUMALT=1;ODDS=1857.5;PAIRED=0.998008;PAIREDR=0.993676;PAO=0;PQA=0;PQR=0;PRO=0;QA=17697;QR=44483;RO=1265;RPL=246;RPP=3.44286;RPPR=34.295;RPR=256;RUN=1;SAF=249;SAP=3.07951;SAR=253;SRF=620;SRP=4.08316;SRR=645;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.4974C>T|p.Tyr1658Tyr|4974/21291|4974/21291|1658/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.4974C>T|p.Tyr1658Tyr|4974/13218|4974/13218|1658/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2520C>T|p.Tyr840Tyr|2520/5835|2520/5835|840/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2520C>T|p.Tyr840Tyr|2520/5835|2520/5835|840/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3316C>T|||||3316|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3316C>T|||||3316|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4816C>T|||||4816|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4816C>T|||||4816|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4434C>T|||||4434|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4434C>T|||||4434|WARNING_TRANSCRIPT_NO_STOP_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2520C>T|||||2520|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2520C>T|||||2520|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1769:1265,502:1265:44483:502:17697:-888.788,0,-3300.25
NC_045512.2	5283	.	AC	GT	3.00147E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=2X;DP=1943;DPB=1943;DPRA=0;EPP=3.0103;EPPR=4.93047;GTI=0;LEN=2;MEANALT=5;MQM=27.9167;MQMR=50.6312;NS=1;NUMALT=1;ODDS=2370.54;PAIRED=0.944444;PAIREDR=0.996318;PAO=0;PQA=0;PQR=0;PRO=0;QA=1258;QR=66807;RO=1901;RPL=24;RPP=11.6962;RPPR=22.019;RPR=12;RUN=1;SAF=16;SAP=3.9754;SAR=20;SRF=946;SRP=3.10282;SRR=955;TYPE=complex;ANN=GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5018_5019delACinsGT|p.Asn1673Ser|5018/21291|5018/21291|1673/7096||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5018_5019delACinsGT|p.Asn1673Ser|5018/13218|5018/13218|1673/4405||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2564_2565delACinsGT|p.Asn855Ser|2564/5835|2564/5835|855/1944||WARNING_TRANSCRIPT_NO_START_CODON,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2564_2565delACinsGT|p.Asn855Ser|2564/5835|2564/5835|855/1944||WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3272_-3271delACinsGT|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3272_-3271delACinsGT|||||3272|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4772_-4771delACinsGT|||||4772|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4772_-4771delACinsGT|||||4772|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4478_*4479delACinsGT|||||4478|WARNING_TRANSCRIPT_NO_STOP_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4478_*4479delACinsGT|||||4478|WARNING_TRANSCRIPT_NO_STOP_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2564_*2565delACinsGT|||||2564|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2564_*2565delACinsGT|||||2564|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1943:1901,36:1901:66807:36:1258:0,-517.448,-5588.85
NC_045512.2	5388	.	C	A	15425.8	.	AB=0.421856;ABP=89.8904;AC=1;AF=0.5;AN=2;AO=691;CIGAR=1X;DP=1638;DPB=1638;DPRA=0;EPP=4.14475;EPPR=3.12289;GTI=0;LEN=1;MEANALT=2;MQM=50.8871;MQMR=52.8868;NS=1;NUMALT=1;ODDS=3551.93;PAIRED=0.994211;PAIREDR=0.996825;PAO=0;PQA=0;PQR=0;PRO=0;QA=24252;QR=33052;RO=945;RPL=343;RPP=3.08886;RPPR=10.476;RPR=348;RUN=1;SAF=347;SAP=3.03858;SAR=344;SRF=484;SRP=4.22586;SRR=461;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5123C>A|p.Ala1708Asp|5123/21291|5123/21291|1708/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5123C>A|p.Ala1708Asp|5123/13218|5123/13218|1708/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2669C>A|p.Ala890Asp|2669/5835|2669/5835|890/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2669C>A|p.Ala890Asp|2669/5835|2669/5835|890/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-3167C>A|||||3167|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-3167C>A|||||3167|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4667C>A|||||4667|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4667C>A|||||4667|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4583C>A|||||4583|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4583C>A|||||4583|WARNING_TRANSCRIPT_NO_STOP_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2669C>A|||||2669|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2669C>A|||||2669|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1638:945,691:945:33052:691:24252:-1559.56,0,-2377.37
NC_045512.2	5584	.	A	G	4302.11	.	AB=0.25588;ABP=729.246;AC=1;AF=0.5;AN=2;AO=359;CIGAR=1X;DP=1403;DPB=1403;DPRA=0;EPP=3.30668;EPPR=3.26222;GTI=0;LEN=1;MEANALT=2;MQM=41.5766;MQMR=50.7507;NS=1;NUMALT=1;ODDS=990.597;PAIRED=1;PAIREDR=0.999041;PAO=0;PQA=0;PQR=0;PRO=0;QA=12643;QR=36358;RO=1043;RPL=241;RPP=94.5206;RPPR=6.51006;RPR=118;RUN=1;SAF=176;SAP=3.30668;SAR=183;SRF=520;SRP=3.02904;SRR=523;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5319A>G|p.Thr1773Thr|5319/21291|5319/21291|1773/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5319A>G|p.Thr1773Thr|5319/13218|5319/13218|1773/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.2865A>G|p.Thr955Thr|2865/5835|2865/5835|955/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.2865A>G|p.Thr955Thr|2865/5835|2865/5835|955/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2971A>G|||||2971|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2971A>G|||||2971|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4471A>G|||||4471|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4471A>G|||||4471|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4779A>G|||||4779|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4779A>G|||||4779|WARNING_TRANSCRIPT_NO_STOP_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*2865A>G|||||2865|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*2865A>G|||||2865|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1403:1043,359:1043:36358:359:12643:-522.975,0,-2660.57
NC_045512.2	5765	.	GG	AC	2.41084E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=2X;DP=638;DPB=639;DPRA=0;EPP=3.20771;EPPR=3.09772;GTI=0;LEN=2;MEANALT=4;MQM=38;MQMR=53.4525;NS=1;NUMALT=1;ODDS=776.345;PAIRED=1;PAIREDR=0.996779;PAO=2;PQA=64;PQR=0;PRO=0;QA=362;QR=21351;RO=621;RPL=1;RPP=19.0002;RPPR=3.04177;RPR=10;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=308;SRP=3.09772;SRR=313;TYPE=complex;ANN=AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5500_5501delGGinsAC|p.Gly1834Thr|5500/21291|5500/21291|1834/7096||,AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5500_5501delGGinsAC|p.Gly1834Thr|5500/13218|5500/13218|1834/4405||,AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3046_3047delGGinsAC|p.Gly1016Thr|3046/5835|3046/5835|1016/1944||WARNING_TRANSCRIPT_NO_START_CODON,AC|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3046_3047delGGinsAC|p.Gly1016Thr|3046/5835|3046/5835|1016/1944||WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2790_-2789delGGinsAC|||||2790|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2790_-2789delGGinsAC|||||2790|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4290_-4289delGGinsAC|||||4290|WARNING_TRANSCRIPT_NO_START_CODON,AC|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4290_-4289delGGinsAC|||||4290|WARNING_TRANSCRIPT_NO_START_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725297.1|protein_coding||c.*4960_*4961delGGinsAC|||||4960|WARNING_TRANSCRIPT_NO_STOP_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742608.1|protein_coding||c.*4960_*4961delGGinsAC|||||4960|WARNING_TRANSCRIPT_NO_STOP_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3046_*3047delGGinsAC|||||3046|WARNING_TRANSCRIPT_NO_START_CODON,AC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3046_*3047delGGinsAC|||||3046|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:638:621,11:621:21351:11:362:0,-164.517,-1844.91
NC_045512.2	5818	.	T	C	5838.01	.	AB=0.4;ABP=59.4686;AC=1;AF=0.5;AN=2;AO=260;CIGAR=1X;DP=650;DPB=650;DPRA=0;EPP=3.04371;EPPR=3.21074;GTI=0;LEN=1;MEANALT=1;MQM=52.7192;MQMR=53.2333;NS=1;NUMALT=1;ODDS=1344.25;PAIRED=1;PAIREDR=0.984615;PAO=0;PQA=0;PQR=0;PRO=0;QA=9096;QR=13642;RO=390;RPL=135;RPP=3.84548;RPPR=7.37552;RPR=125;RUN=1;SAF=130;SAP=3.0103;SAR=130;SRF=197;SRP=3.09939;SRR=193;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5553T>C|p.Ala1851Ala|5553/21291|5553/21291|1851/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5553T>C|p.Ala1851Ala|5553/13218|5553/13218|1851/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3099T>C|p.Ala1033Ala|3099/5835|3099/5835|1033/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3099T>C|p.Ala1033Ala|3099/5835|3099/5835|1033/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2737T>C|||||2737|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2737T>C|||||2737|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4237T>C|||||4237|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4237T>C|||||4237|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3099T>C|||||3099|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3099T>C|||||3099|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:650:390,260:390:13642:260:9096:-596.985,0,-994.554
NC_045512.2	5909	.	TAT	TT	0.0	.	AB=0.156273;ABP=1401.75;AC=1;AF=0.5;AN=2;AO=213;CIGAR=1M1D1M;DP=1363;DPB=1294.33;DPRA=0;EPP=5.30411;EPPR=6.83731;GTI=0;LEN=1;MEANALT=2;MQM=35.23;MQMR=50.8407;NS=1;NUMALT=1;ODDS=246.516;PAIRED=1;PAIREDR=0.996519;PAO=3.5;PQA=115.5;PQR=115.5;PRO=3.5;QA=7203;QR=39975;RO=1149;RPL=22;RPP=294.181;RPPR=95.3139;RPR=191;RUN=1;SAF=114;SAP=5.30411;SAR=99;SRF=595;SRP=6.18719;SRR=554;TYPE=del;ANN=TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5645delA|p.Tyr1882fs|5645/21291|5645/21291|1882/7096||,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5645delA|p.Tyr1882fs|5645/13218|5645/13218|1882/4405||,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3191delA|p.Tyr1064fs|3191/5835|3191/5835|1064/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3191delA|p.Tyr1064fs|3191/5835|3191/5835|1064/1944||WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2645delA|||||2645|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2645delA|||||2645|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4145delA|||||4145|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4145delA|||||4145|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3191delA|||||3191|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3191delA|||||3191|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1363:1149,213:1149:39975:213:7203:-87.388,0,-2987.82
NC_045512.2	5944	.	C	T	3592.72	.	AB=0.230724;ABP=1081.24;AC=1;AF=0.5;AN=2;AO=395;CIGAR=1X;DP=1712;DPB=1712;DPRA=0;EPP=3.93936;EPPR=5.52194;GTI=0;LEN=1;MEANALT=2;MQM=38.6253;MQMR=51.3338;NS=1;NUMALT=1;ODDS=827.255;PAIRED=1;PAIREDR=0.996198;PAO=0;PQA=0;PQR=0;PRO=0;QA=13976;QR=46014;RO=1315;RPL=120;RPP=135.085;RPPR=20.529;RPR=275;RUN=1;SAF=205;SAP=4.24721;SAR=190;SRF=665;SRP=3.38184;SRR=650;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5679C>T|p.Asp1893Asp|5679/21291|5679/21291|1893/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5679C>T|p.Asp1893Asp|5679/13218|5679/13218|1893/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3225C>T|p.Asp1075Asp|3225/5835|3225/5835|1075/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3225C>T|p.Asp1075Asp|3225/5835|3225/5835|1075/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2611C>T|||||2611|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2611C>T|||||2611|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4111C>T|||||4111|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4111C>T|||||4111|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3225C>T|||||3225|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3225C>T|||||3225|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1712:1315,395:1315:46014:395:13976:-494.233,0,-3429.74
NC_045512.2	5986	.	CACAG	TACAA,TACAG	13031.4	.	AB=0.329331,0.288165;ABP=445.51,684.722;AC=1,0;AF=0.5,0;AN=2;AO=576,504;CIGAR=1X3M1X,1X4M;DP=1749;DPB=1765.2;DPRA=0,0;EPP=3.25157,3.02753;EPPR=3.09318;GTI=0;LEN=5,1;MEANALT=8,8;MQM=48.3976,43.7917;MQMR=52.0015;NS=1;NUMALT=2;ODDS=771.741;PAIRED=0.996528,0.996032;PAIREDR=0.996947;PAO=55,26;PQA=1715.5,887.5;PQR=0;PRO=0;QA=20335,15262;QR=22850;RO=655;RPL=279,257;RPP=4.23175,3.44115;RPPR=8.05276;RPR=297,247;RUN=1,1;SAF=287,256;SAP=3.02538,3.28604;SAR=289,248;SRF=333;SRP=3.41144;SRR=322;TYPE=complex,snp;ANN=TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721_5725delCACAGinsTACAA|p.Glu1909Lys|5721/21291|5721/21291|1907/7096||,TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5721_5725delCACAGinsTACAA|p.Glu1909Lys|5721/13218|5721/13218|1907/4405||,TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3267_3271delCACAGinsTACAA|p.Glu1091Lys|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,TACAA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3267_3271delCACAGinsTACAA|p.Glu1091Lys|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,TACAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.5721C>T|p.Phe1907Phe|5721/21291|5721/21291|1907/7096||,TACAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.5721C>T|p.Phe1907Phe|5721/13218|5721/13218|1907/4405||,TACAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3267C>T|p.Phe1089Phe|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,TACAG|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3267C>T|p.Phe1089Phe|3267/5835|3267/5835|1089/1944||WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2569C>T|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2569_-2565delCACAGinsTACAA|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2569C>T|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2569_-2565delCACAGinsTACAA|||||2569|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4069C>T|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-4069_-4065delCACAGinsTACAA|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4069C>T|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-4069_-4065delCACAGinsTACAA|||||4069|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4987C>T|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4987_-4983delCACAGinsTACAA|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4987C>T|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4987_-4983delCACAGinsTACAA|||||4987|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3267C>T|||||3267|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3267_*3271delCACAGinsTACAA|||||3267|WARNING_TRANSCRIPT_NO_START_CODON,TACAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3267C>T|||||3267|WARNING_TRANSCRIPT_NO_START_CODON,TACAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3267_*3271delCACAGinsTACAA|||||3267|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1749:655,576,504:655:22850:576,504:20335,15262:-1312.47,0,-1588.23,-332.158,-584.148,-1942.05
NC_045512.2	6401	.	CC	GT,CT	41378.4	.	AB=0.0133511,0.5751;ABP=6165.94,149.78;AC=0,1;AF=0,0.5;AN=2;AO=40,1723;CIGAR=2X,1M1X;DP=2996;DPB=2997;DPRA=0,0;EPP=3.0103,4.92719;EPPR=4.20567;GTI=0;LEN=2,1;MEANALT=5,5;MQM=50.125,50.3186;MQMR=53.1954;NS=1;NUMALT=2;ODDS=6500.05;PAIRED=1,0.993035;PAIREDR=0.989414;PAO=1.5,0.5;PQA=48,16;PQR=0;PRO=0;QA=1416,60413;QR=42916;RO=1228;RPL=23,837;RPP=4.96463,6.03625;RPPR=51.7376;RPR=17,886;RUN=1,1;SAF=19,845;SAP=3.22745,4.38275;SAR=21,878;SRF=606;SRP=3.46298;SRR=622;TYPE=complex,snp;ANN=CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6137C>T|p.Pro2046Leu|6137/21291|6137/21291|2046/7096||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6136_6137delCCinsGT|p.Pro2046Val|6136/21291|6136/21291|2046/7096||,CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6137C>T|p.Pro2046Leu|6137/13218|6137/13218|2046/4405||,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6136_6137delCCinsGT|p.Pro2046Val|6136/13218|6136/13218|2046/4405||,CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3683C>T|p.Pro1228Leu|3683/5835|3683/5835|1228/1944||WARNING_TRANSCRIPT_NO_START_CODON,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3682_3683delCCinsGT|p.Pro1228Val|3682/5835|3682/5835|1228/1944||WARNING_TRANSCRIPT_NO_START_CODON,CT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3683C>T|p.Pro1228Leu|3683/5835|3683/5835|1228/1944||WARNING_TRANSCRIPT_NO_START_CODON,GT|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3682_3683delCCinsGT|p.Pro1228Val|3682/5835|3682/5835|1228/1944||WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2154_-2153delCCinsGT|||||2154|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2153C>T|||||2153|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2154_-2153delCCinsGT|||||2154|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2153C>T|||||2153|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3654_-3653delCCinsGT|||||3654|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3653C>T|||||3653|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3654_-3653delCCinsGT|||||3654|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3653C>T|||||3653|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4572_-4571delCCinsGT|||||4572|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4571C>T|||||4571|WARNING_TRANSCRIPT_NO_START_CODON,GT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4572_-4571delCCinsGT|||||4572|WARNING_TRANSCRIPT_NO_START_CODON,CT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4571C>T|||||4571|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3682_*3683delCCinsGT|||||3682|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3683C>T|||||3683|WARNING_TRANSCRIPT_NO_START_CODON,GT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3682_*3683delCCinsGT|||||3682|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3683C>T|||||3683|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/2:2996:1228,40,1723:1228:42916:40,1723:1416,60413:-4165.56,-4430.39,-7791.85,0,-3268.69,-2854.85
NC_045512.2	6459	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=47;CIGAR=1X;DP=2778;DPB=2778;DPRA=0;EPP=3.42611;EPPR=9.88729;GTI=0;LEN=1;MEANALT=1;MQM=40.6809;MQMR=52.4357;NS=1;NUMALT=1;ODDS=3365.28;PAIRED=0.595745;PAIREDR=0.992677;PAO=0;PQA=0;PQR=0;PRO=0;QA=1642;QR=96439;RO=2731;RPL=0;RPP=105.07;RPPR=159.052;RPR=47;RUN=1;SAF=22;SAP=3.42611;SAR=25;SRF=1324;SRP=8.48788;SRR=1407;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6194A>G|p.Asn2065Ser|6194/21291|6194/21291|2065/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6194A>G|p.Asn2065Ser|6194/13218|6194/13218|2065/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3740A>G|p.Asn1247Ser|3740/5835|3740/5835|1247/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3740A>G|p.Asn1247Ser|3740/5835|3740/5835|1247/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-2096A>G|||||2096|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-2096A>G|||||2096|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3596A>G|||||3596|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3596A>G|||||3596|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4514A>G|||||4514|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4514A>G|||||4514|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3740A>G|||||3740|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3740A>G|||||3740|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2778:2731,47:2731:96439:47:1642:0,-709.432,-8216.17
NC_045512.2	6581	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3950;DPB=3950;DPRA=0;EPP=3.0103;EPPR=9.87224;GTI=0;LEN=1;MEANALT=2;MQM=53.7143;MQMR=53.3706;NS=1;NUMALT=1;ODDS=4948;PAIRED=1;PAIREDR=0.99051;PAO=0;PQA=0;PQR=0;PRO=0;QA=1448;QR=137583;RO=3899;RPL=24;RPP=4.87156;RPPR=11.4361;RPR=18;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1980;SRP=5.08264;SRR=1919;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6316A>G|p.Thr2106Ala|6316/21291|6316/21291|2106/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6316A>G|p.Thr2106Ala|6316/13218|6316/13218|2106/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3862A>G|p.Thr1288Ala|3862/5835|3862/5835|1288/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3862A>G|p.Thr1288Ala|3862/5835|3862/5835|1288/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1974A>G|||||1974|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1974A>G|||||1974|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3474A>G|||||3474|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3474A>G|||||3474|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4392A>G|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4392A>G|||||4392|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3862A>G|||||3862|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3862A>G|||||3862|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3950:3899,42:3899:137583:42:1448:0,-1057.38,-11906.7
NC_045512.2	6654	.	TTAATAGTGTCCCTTGGGATACTATAGCT	TT	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=90;CIGAR=1M27D1M;DP=2584;DPB=2502.62;DPRA=0;EPP=3.87889;EPPR=3.33544;GTI=0;LEN=27;MEANALT=41;MQM=49.5111;MQMR=53.8523;NS=1;NUMALT=1;ODDS=2613.21;PAIRED=1;PAIREDR=0.994608;PAO=8;PQA=245;PQR=626;PRO=23;QA=2527;QR=83585;RO=2411;RPL=56;RPP=14.688;RPPR=13.7109;RPR=34;RUN=1;SAF=44;SAP=3.10681;SAR=46;SRF=1215;SRP=3.33544;SRR=1196;TYPE=del;ANN=TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6394_6420delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser2132_Asn2140del|6394/21291|6394/21291|2132/7096||INFO_REALIGN_3_PRIME,TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6394_6420delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser2132_Asn2140del|6394/13218|6394/13218|2132/4405||INFO_REALIGN_3_PRIME,TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.3940_3966delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser1314_Asn1322del|3940/5835|3940/5835|1314/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,TT|conservative_inframe_deletion|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.3940_3966delAGTGTCCCTTGGGATACTATAGCTAAT|p.Ser1314_Asn1322del|3940/5835|3940/5835|1314/1944||WARNING_TRANSCRIPT_NO_START_CODON&INFO_REALIGN_3_PRIME,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1899_-1873delAATAGTGTCCCTTGGGATACTATAGCT|||||1899|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1899_-1873delAATAGTGTCCCTTGGGATACTATAGCT|||||1899|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3399_-3373delAATAGTGTCCCTTGGGATACTATAGCT|||||3399|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3399_-3373delAATAGTGTCCCTTGGGATACTATAGCT|||||3399|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4317_-4291delAATAGTGTCCCTTGGGATACTATAGCT|||||4317|WARNING_TRANSCRIPT_NO_START_CODON,TT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4317_-4291delAATAGTGTCCCTTGGGATACTATAGCT|||||4317|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*3937_*3963delAATAGTGTCCCTTGGGATACTATAGCT|||||3937|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*3937_*3963delAATAGTGTCCCTTGGGATACTATAGCT|||||3937|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2584:2411,90:2411:83585:90:2527:0,-542.491,-7120.65
NC_045512.2	6728	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X;DP=4495;DPB=4495;DPRA=0;EPP=3.02688;EPPR=3.0347;GTI=0;LEN=1;MEANALT=3;MQM=52.626;MQMR=52.7916;NS=1;NUMALT=1;ODDS=4749.06;PAIRED=0.984733;PAIREDR=0.984637;PAO=0;PQA=0;PQR=0;PRO=0;QA=4607;QR=153668;RO=4361;RPL=65;RPP=3.02688;RPPR=567.775;RPR=66;RUN=1;SAF=63;SAP=3.4247;SAR=68;SRF=2187;SRP=3.09445;SRR=2174;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6463A>G|p.Asn2155Asp|6463/21291|6463/21291|2155/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6463A>G|p.Asn2155Asp|6463/13218|6463/13218|2155/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4009A>G|p.Asn1337Asp|4009/5835|4009/5835|1337/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4009A>G|p.Asn1337Asp|4009/5835|4009/5835|1337/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1827A>G|||||1827|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1827A>G|||||1827|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3327A>G|||||3327|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3327A>G|||||3327|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4245A>G|||||4245|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4245A>G|||||4245|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4009A>G|||||4009|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4009A>G|||||4009|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4495:4361,131:4361:153668:131:4607:0,-960.457,-12910.3
NC_045512.2	6772	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=72;CIGAR=1X;DP=5961;DPB=5961;DPRA=0;EPP=3.13094;EPPR=4.2522;GTI=0;LEN=1;MEANALT=3;MQM=47.5833;MQMR=51.9471;NS=1;NUMALT=1;ODDS=7432.86;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2518;QR=206887;RO=5882;RPL=9;RPP=90.9549;RPPR=574.318;RPR=63;RUN=1;SAF=38;SAP=3.49285;SAR=34;SRF=2959;SRP=3.48875;SRR=2923;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6507G>A|p.Met2169Ile|6507/21291|6507/21291|2169/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6507G>A|p.Met2169Ile|6507/13218|6507/13218|2169/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4053G>A|p.Met1351Ile|4053/5835|4053/5835|1351/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4053G>A|p.Met1351Ile|4053/5835|4053/5835|1351/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1783G>A|||||1783|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1783G>A|||||1783|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3283G>A|||||3283|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3283G>A|||||3283|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4201G>A|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4201G>A|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4053G>A|||||4053|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4053G>A|||||4053|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5961:5882,72:5882:206887:72:2518:0,-1588.67,-17552.3
NC_045512.2	6954	.	T	C	78261.2	.	AB=0.74609;ABP=2290.15;AC=1;AF=0.5;AN=2;AO=3244;CIGAR=1X;DP=4348;DPB=4348;DPRA=0;EPP=3.39586;EPPR=3.51658;GTI=0;LEN=1;MEANALT=3;MQM=49.9263;MQMR=53.5255;NS=1;NUMALT=1;ODDS=4109.19;PAIRED=0.99476;PAIREDR=0.993625;PAO=0;PQA=0;PQR=0;PRO=0;QA=112718;QR=38145;RO=1098;RPL=1650;RPP=5.10948;RPPR=11.1108;RPR=1594;RUN=1;SAF=1620;SAP=3.02101;SAR=1624;SRF=546;SRP=3.0815;SRR=552;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6689T>C|p.Ile2230Thr|6689/21291|6689/21291|2230/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6689T>C|p.Ile2230Thr|6689/13218|6689/13218|2230/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4235T>C|p.Ile1412Thr|4235/5835|4235/5835|1412/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4235T>C|p.Ile1412Thr|4235/5835|4235/5835|1412/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1601T>C|||||1601|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1601T>C|||||1601|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-3101T>C|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-3101T>C|||||3101|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-4019T>C|||||4019|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-4019T>C|||||4019|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4889T>C|||||4889|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4889T>C|||||4889|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4235T>C|||||4235|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4235T>C|||||4235|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4348:1098,3244:1098:38145:3244:112718:-8076.53,0,-2034.93
NC_045512.2	7124	.	C	T	36735.9	.	AB=0.593619;ABP=203.456;AC=1;AF=0.5;AN=2;AO=1563;CIGAR=1X;DP=2633;DPB=2633;DPRA=0;EPP=3.87861;EPPR=6.09993;GTI=0;LEN=1;MEANALT=2;MQM=48.3762;MQMR=52.6707;NS=1;NUMALT=1;ODDS=5513.12;PAIRED=0.997441;PAIREDR=0.992516;PAO=0;PQA=0;PQR=0;PRO=0;QA=55234;QR=37290;RO=1069;RPL=642;RPP=111.155;RPPR=68.0956;RPR=921;RUN=1;SAF=815;SAP=9.24686;SAR=748;SRF=544;SRP=3.7436;SRR=525;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6859C>T|p.Pro2287Ser|6859/21291|6859/21291|2287/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6859C>T|p.Pro2287Ser|6859/13218|6859/13218|2287/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4405C>T|p.Pro1469Ser|4405/5835|4405/5835|1469/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4405C>T|p.Pro1469Ser|4405/5835|4405/5835|1469/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1431C>T|||||1431|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1431C>T|||||1431|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2931C>T|||||2931|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2931C>T|||||2931|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3849C>T|||||3849|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3849C>T|||||3849|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4719C>T|||||4719|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4719C>T|||||4719|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4968C>T|||||4968|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4968C>T|||||4968|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4405C>T|||||4405|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4405C>T|||||4405|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2633:1069,1563:1069:37290:1563:55234:-3714.31,0,-2430.12
NC_045512.2	7262	.	C	A	7.353E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=2907;DPB=2907;DPRA=0;EPP=32.2045;EPPR=8.10485;GTI=0;LEN=1;MEANALT=2;MQM=54.75;MQMR=52.6598;NS=1;NUMALT=1;ODDS=3772.74;PAIRED=1;PAIREDR=0.995813;PAO=0;PQA=0;PQR=0;PRO=0;QA=526;QR=95172;RO=2866;RPL=29;RPP=32.2045;RPPR=29.2225;RPR=7;RUN=1;SAF=36;SAP=81.1833;SAR=0;SRF=1432;SRP=3.01333;SRR=1434;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.6997C>A|p.Leu2333Ile|6997/21291|6997/21291|2333/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.6997C>A|p.Leu2333Ile|6997/13218|6997/13218|2333/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4543C>A|p.Leu1515Ile|4543/5835|4543/5835|1515/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4543C>A|p.Leu1515Ile|4543/5835|4543/5835|1515/1944||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1293C>A|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1293C>A|||||1293|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2793C>A|||||2793|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2793C>A|||||2793|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3711C>A|||||3711|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3711C>A|||||3711|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4581C>A|||||4581|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4581C>A|||||4581|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4830C>A|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4830C>A|||||4830|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4543C>A|||||4543|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4543C>A|||||4543|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2907:2866,36:2866:95172:36:526:0,-827.217,-8169.18
NC_045512.2	7363	.	G	C	2.6519E-13	.	AB=0.121355;ABP=3974.32;AC=1;AF=0.5;AN=2;AO=387;CIGAR=1X;DP=3189;DPB=3189;DPRA=0;EPP=3.46479;EPPR=5.99569;GTI=0;LEN=1;MEANALT=3;MQM=45.4703;MQMR=50.912;NS=1;NUMALT=1;ODDS=883.768;PAIRED=0.994832;PAIREDR=0.995351;PAO=0;PQA=0;PQR=0;PRO=0;QA=13459;QR=98261;RO=2796;RPL=311;RPP=312.88;RPPR=63.0318;RPR=76;RUN=1;SAF=189;SAP=3.46479;SAR=198;SRF=1396;SRP=3.02273;SRR=1400;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7098G>C|p.Trp2366Cys|7098/21291|7098/21291|2366/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7098G>C|p.Trp2366Cys|7098/13218|7098/13218|2366/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4644G>C|p.Trp1548Cys|4644/5835|4644/5835|1548/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4644G>C|p.Trp1548Cys|4644/5835|4644/5835|1548/1944||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1192G>C|||||1192|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1192G>C|||||1192|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2692G>C|||||2692|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2692G>C|||||2692|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3610G>C|||||3610|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3610G>C|||||3610|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4480G>C|||||4480|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4480G>C|||||4480|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4729G>C|||||4729|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4729G>C|||||4729|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4644G>C|||||4644|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4644G>C|||||4644|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3189:2796,387:2796:98261:387:13459:-103.873,0,-7409.47
NC_045512.2	7429	.	A	G	17852.7	.	AB=0.408913;ABP=150.168;AC=1;AF=0.5;AN=2;AO=835;CIGAR=1X;DP=2042;DPB=2042;DPRA=0;EPP=4.15715;EPPR=4.42428;GTI=0;LEN=1;MEANALT=2;MQM=50.1353;MQMR=52.887;NS=1;NUMALT=1;ODDS=4110.74;PAIRED=0.99521;PAIREDR=0.994186;PAO=0;PQA=0;PQR=0;PRO=0;QA=28871;QR=42302;RO=1204;RPL=398;RPP=6.96576;RPPR=4.2295;RPR=437;RUN=1;SAF=423;SAP=3.32497;SAR=412;SRF=613;SRP=3.88322;SRR=591;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7164A>G|p.Ala2388Ala|7164/21291|7164/21291|2388/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7164A>G|p.Ala2388Ala|7164/13218|7164/13218|2388/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.4710A>G|p.Ala1570Ala|4710/5835|4710/5835|1570/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.4710A>G|p.Ala1570Ala|4710/5835|4710/5835|1570/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-1126A>G|||||1126|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-1126A>G|||||1126|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-2626A>G|||||2626|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-2626A>G|||||2626|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-3544A>G|||||3544|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-3544A>G|||||3544|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-4414A>G|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-4414A>G|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-4663A>G|||||4663|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-4663A>G|||||4663|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725298.1|protein_coding||c.*4710A>G|||||4710|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742609.1|protein_coding||c.*4710A>G|||||4710|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2042:1204,835:1204:42302:835:28871:-1808.82,0,-3057.19
NC_045512.2	8172	.	C	T	7.05188E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=841;DPB=841;DPRA=0;EPP=3.13803;EPPR=3.02084;GTI=0;LEN=1;MEANALT=1;MQM=50.0588;MQMR=52.818;NS=1;NUMALT=1;ODDS=984.169;PAIRED=1;PAIREDR=0.970874;PAO=0;PQA=0;PQR=0;PRO=0;QA=577;QR=28651;RO=824;RPL=11;RPP=6.20364;RPPR=7.22675;RPR=6;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=419;SRP=3.52682;SRR=405;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.7907C>T|p.Ala2636Val|7907/21291|7907/21291|2636/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.7907C>T|p.Ala2636Val|7907/13218|7907/13218|2636/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5453C>T|p.Ala1818Val|5453/5835|5453/5835|1818/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5453C>T|p.Ala1818Val|5453/5835|5453/5835|1818/1944||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-383C>T|||||383|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-383C>T|||||383|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1883C>T|||||1883|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1883C>T|||||1883|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2801C>T|||||2801|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2801C>T|||||2801|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3671C>T|||||3671|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3671C>T|||||3671|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3920C>T|||||3920|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3920C>T|||||3920|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4514C>T|||||4514|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4514C>T|||||4514|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4853C>T|||||4853|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4853C>T|||||4853|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:841:824,17:824:28651:17:577:0,-204.864,-2432.99
NC_045512.2	8364	.	A	G	8004.45	.	AB=0.408027;ABP=68.917;AC=1;AF=0.5;AN=2;AO=366;CIGAR=1X;DP=897;DPB=897;DPRA=0;EPP=3.0103;EPPR=3.27252;GTI=0;LEN=1;MEANALT=2;MQM=50.4071;MQMR=53.6094;NS=1;NUMALT=1;ODDS=1843.09;PAIRED=1;PAIREDR=0.992453;PAO=0;PQA=0;PQR=0;PRO=0;QA=12874;QR=18616;RO=530;RPL=173;RPP=5.38349;RPPR=9.56569;RPR=193;RUN=1;SAF=184;SAP=3.03403;SAR=182;SRF=268;SRP=3.1578;SRR=262;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8099A>G|p.Asn2700Ser|8099/21291|8099/21291|2700/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8099A>G|p.Asn2700Ser|8099/13218|8099/13218|2700/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding|1/1|c.5645A>G|p.Asn1882Ser|5645/5835|5645/5835|1882/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding|1/1|c.5645A>G|p.Asn1882Ser|5645/5835|5645/5835|1882/1944||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.-191A>G|||||191|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.-191A>G|||||191|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1691A>G|||||1691|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1691A>G|||||1691|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2609A>G|||||2609|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2609A>G|||||2609|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3479A>G|||||3479|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3479A>G|||||3479|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3728A>G|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3728A>G|||||3728|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4322A>G|||||4322|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4322A>G|||||4322|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4661A>G|||||4661|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4661A>G|||||4661|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:897:530,366:530:18616:366:12874:-814.947,0,-1355.26
NC_045512.2	8557	.	A	G	7207.18	.	AB=0.361084;ABP=176.158;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1033;DPB=1033;DPRA=0;EPP=3.29556;EPPR=4.60271;GTI=0;LEN=1;MEANALT=1;MQM=46.622;MQMR=52.8197;NS=1;NUMALT=1;ODDS=1659.51;PAIRED=0.991957;PAIREDR=0.993939;PAO=0;PQA=0;PQR=0;PRO=0;QA=13232;QR=23292;RO=660;RPL=194;RPP=4.32017;RPPR=3.85257;RPR=179;RUN=1;SAF=178;SAP=4.69275;SAR=195;SRF=321;SRP=4.0763;SRR=339;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8292A>G|p.Lys2764Lys|8292/21291|8292/21291|2764/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8292A>G|p.Lys2764Lys|8292/13218|8292/13218|2764/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.3A>G|p.Lys1Lys|3/1500|3/1500|1/499||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.3A>G|p.Lys1Lys|3/1500|3/1500|1/499||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1498A>G|||||1498|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1498A>G|||||1498|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2416A>G|||||2416|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2416A>G|||||2416|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3286A>G|||||3286|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3286A>G|||||3286|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3535A>G|||||3535|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3535A>G|||||3535|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4129A>G|||||4129|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4129A>G|||||4129|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4468A>G|||||4468|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4468A>G|||||4468|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4885A>G|||||4885|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4885A>G|||||4885|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3A>G|||||3|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3A>G|||||3|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1033:660,373:660:23292:373:13232:-746.33,0,-1718.1
NC_045512.2	8565	.	ATAA	GTAG	5776.02	.	AB=0.3433;ABP=195.603;AC=1;AF=0.5;AN=2;AO=310;CIGAR=1X2M1X;DP=903;DPB=910;DPRA=0;EPP=3.0103;EPPR=5.48989;GTI=0;LEN=4;MEANALT=2;MQM=46.2516;MQMR=53.3649;NS=1;NUMALT=1;ODDS=1329.98;PAIRED=0.987097;PAIREDR=0.996622;PAO=26;PQA=880;PQR=0;PRO=2;QA=11017;QR=20793;RO=592;RPL=153;RPP=3.12238;RPPR=17.1102;RPR=157;RUN=1;SAF=152;SAP=3.26247;SAR=158;SRF=288;SRP=3.94932;SRR=304;TYPE=complex;ANN=GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8300_8303delATAAinsGTAG|p.AsnAsn2767SerSer|8300/21291|8300/21291|2767/7096||,GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8300_8303delATAAinsGTAG|p.AsnAsn2767SerSer|8300/13218|8300/13218|2767/4405||,GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.11_14delATAAinsGTAG|p.AsnAsn4SerSer|11/1500|11/1500|4/499||WARNING_TRANSCRIPT_NO_START_CODON,GTAG|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.11_14delATAAinsGTAG|p.AsnAsn4SerSer|11/1500|11/1500|4/499||WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1490_-1487delATAAinsGTAG|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1490_-1487delATAAinsGTAG|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2408_-2405delATAAinsGTAG|||||2408|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2408_-2405delATAAinsGTAG|||||2408|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3278_-3275delATAAinsGTAG|||||3278|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3278_-3275delATAAinsGTAG|||||3278|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3527_-3524delATAAinsGTAG|||||3527|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3527_-3524delATAAinsGTAG|||||3527|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4121_-4118delATAAinsGTAG|||||4121|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4121_-4118delATAAinsGTAG|||||4121|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4460_-4457delATAAinsGTAG|||||4460|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4460_-4457delATAAinsGTAG|||||4460|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4877_-4874delATAAinsGTAG|||||4877|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4877_-4874delATAAinsGTAG|||||4877|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*11_*14delATAAinsGTAG|||||11|WARNING_TRANSCRIPT_NO_START_CODON,GTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*11_*14delATAAinsGTAG|||||11|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:903:592,310:592:20793:310:11017:-604.693,0,-1551.51
NC_045512.2	8634	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=694;DPB=694;DPRA=0;EPP=3.7749;EPPR=6.1523;GTI=0;LEN=1;MEANALT=2;MQM=47.1831;MQMR=51.8006;NS=1;NUMALT=1;ODDS=331.413;PAIRED=0.971831;PAIREDR=0.96463;PAO=0;PQA=0;PQR=0;PRO=0;QA=2483;QR=21417;RO=622;RPL=71;RPP=157.185;RPPR=178.18;RPR=0;RUN=1;SAF=33;SAP=3.7749;SAR=38;SRF=307;SRP=3.23373;SRR=315;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8369T>C|p.Ile2790Thr|8369/21291|8369/21291|2790/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8369T>C|p.Ile2790Thr|8369/13218|8369/13218|2790/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.80T>C|p.Ile27Thr|80/1500|80/1500|27/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.80T>C|p.Ile27Thr|80/1500|80/1500|27/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1421T>C|||||1421|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1421T>C|||||1421|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2339T>C|||||2339|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2339T>C|||||2339|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3209T>C|||||3209|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3209T>C|||||3209|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3458T>C|||||3458|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3458T>C|||||3458|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-4052T>C|||||4052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-4052T>C|||||4052|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4391T>C|||||4391|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4391T>C|||||4391|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4808T>C|||||4808|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4808T>C|||||4808|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*80T>C|||||80|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*80T>C|||||80|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:694:622,71:622:21417:71:2483:0,-7.8921,-1639.83
NC_045512.2	8716	.	TC	GA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=5;CIGAR=2X;DP=265;DPB=265;DPRA=0;EPP=3.44459;EPPR=3.84548;GTI=0;LEN=2;MEANALT=1;MQM=46.6;MQMR=54.0346;NS=1;NUMALT=1;ODDS=322.356;PAIRED=0.8;PAIREDR=0.965385;PAO=0;PQA=0;PQR=0;PRO=0;QA=178;QR=9081;RO=260;RPL=0;RPP=13.8677;RPPR=3.54482;RPR=5;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=131;SRP=3.04371;SRR=129;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8451_8452delTCinsGA|p.Arg2818Ser|8451/21291|8451/21291|2817/7096||,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8451_8452delTCinsGA|p.Arg2818Ser|8451/13218|8451/13218|2817/4405||,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.162_163delTCinsGA|p.Arg55Ser|162/1500|162/1500|54/499||WARNING_TRANSCRIPT_NO_START_CODON,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.162_163delTCinsGA|p.Arg55Ser|162/1500|162/1500|54/499||WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1339_-1338delTCinsGA|||||1339|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1339_-1338delTCinsGA|||||1339|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2257_-2256delTCinsGA|||||2257|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2257_-2256delTCinsGA|||||2257|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3127_-3126delTCinsGA|||||3127|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3127_-3126delTCinsGA|||||3127|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3376_-3375delTCinsGA|||||3376|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3376_-3375delTCinsGA|||||3376|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3970_-3969delTCinsGA|||||3970|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3970_-3969delTCinsGA|||||3970|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4309_-4308delTCinsGA|||||4309|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4309_-4308delTCinsGA|||||4309|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4726_-4725delTCinsGA|||||4726|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4726_-4725delTCinsGA|||||4726|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*162_*163delTCinsGA|||||162|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*162_*163delTCinsGA|||||162|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:265:260,5:260:9081:5:178:0,-65.7297,-782.204
NC_045512.2	8782	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=295;DPB=295;DPRA=0;EPP=3.0103;EPPR=3.07746;GTI=0;LEN=1;MEANALT=1;MQM=56.5;MQMR=53.7766;NS=1;NUMALT=1;ODDS=368.964;PAIRED=1;PAIREDR=0.979381;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=10001;RO=291;RPL=0;RPP=11.6962;RPPR=3.37594;RPR=4;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=140;SRP=3.91321;SRR=151;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8517C>A|p.Ser2839Arg|8517/21291|8517/21291|2839/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8517C>A|p.Ser2839Arg|8517/13218|8517/13218|2839/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.228C>A|p.Ser76Arg|228/1500|228/1500|76/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.228C>A|p.Ser76Arg|228/1500|228/1500|76/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1273C>A|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1273C>A|||||1273|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2191C>A|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2191C>A|||||2191|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-3061C>A|||||3061|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-3061C>A|||||3061|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3310C>A|||||3310|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3310C>A|||||3310|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3904C>A|||||3904|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3904C>A|||||3904|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4243C>A|||||4243|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4243C>A|||||4243|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4660C>A|||||4660|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4660C>A|||||4660|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*228C>A|||||228|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*228C>A|||||228|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:295:291,4:291:10001:4:140:0,-75.8695,-867.135
NC_045512.2	8844	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=330;DPB=330;DPRA=0;EPP=3.0103;EPPR=3.03761;GTI=0;LEN=1;MEANALT=1;MQM=44.6667;MQMR=51.5503;NS=1;NUMALT=1;ODDS=343.81;PAIRED=0.666667;PAIREDR=0.943396;PAO=0;PQA=0;PQR=0;PRO=0;QA=432;QR=11050;RO=318;RPL=0;RPP=29.068;RPPR=3.44733;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=151;SRP=4.7584;SRR=167;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8579G>A|p.Arg2860Lys|8579/21291|8579/21291|2860/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8579G>A|p.Arg2860Lys|8579/13218|8579/13218|2860/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.290G>A|p.Arg97Lys|290/1500|290/1500|97/499||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.290G>A|p.Arg97Lys|290/1500|290/1500|97/499||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1211G>A|||||1211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1211G>A|||||1211|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2129G>A|||||2129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2129G>A|||||2129|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2999G>A|||||2999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2999G>A|||||2999|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3248G>A|||||3248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3248G>A|||||3248|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3842G>A|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3842G>A|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4181G>A|||||4181|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4181G>A|||||4181|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4598G>A|||||4598|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4598G>A|||||4598|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*290G>A|||||290|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*290G>A|||||290|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:330:318,12:318:11050:12:432:0,-64.5233,-902.184
NC_045512.2	8873	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=3;CIGAR=1X;DP=293;DPB=293;DPRA=0;EPP=3.73412;EPPR=3.61891;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=52.3633;NS=1;NUMALT=1;ODDS=376.316;PAIRED=0.333333;PAIREDR=0.955017;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=9921;RO=289;RPL=3;RPP=9.52472;RPPR=3.01781;RPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=139;SRP=3.91946;SRR=150;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8608C>T|p.Pro2870Ser|8608/21291|8608/21291|2870/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8608C>T|p.Pro2870Ser|8608/13218|8608/13218|2870/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.319C>T|p.Pro107Ser|319/1500|319/1500|107/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.319C>T|p.Pro107Ser|319/1500|319/1500|107/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1182C>T|||||1182|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1182C>T|||||1182|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-2100C>T|||||2100|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-2100C>T|||||2100|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2970C>T|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2970C>T|||||2970|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3219C>T|||||3219|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3219C>T|||||3219|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3813C>T|||||3813|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3813C>T|||||3813|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4152C>T|||||4152|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4152C>T|||||4152|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4569C>T|||||4569|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4569C>T|||||4569|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*319C>T|||||319|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*319C>T|||||319|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:293:289,3:289:9921:3:104:0,-78.3896,-844.462
NC_045512.2	8986	.	C	T	19981.1	.	AB=0.873913;ABP=1120.24;AC=1;AF=0.5;AN=2;AO=804;CIGAR=1X;DP=920;DPB=920;DPRA=0;EPP=3.53966;EPPR=3.0103;GTI=0;LEN=1;MEANALT=3;MQM=49.1704;MQMR=53.2895;NS=1;NUMALT=1;ODDS=139.322;PAIRED=0.992537;PAIREDR=0.991228;PAO=0;PQA=0;PQR=0;PRO=0;QA=28119;QR=3988;RO=114;RPL=329;RPP=60.5813;RPPR=3.0103;RPR=475;RUN=1;SAF=414;SAP=4.56598;SAR=390;SRF=60;SRP=3.69603;SRR=54;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8721C>T|p.Asp2907Asp|8721/21291|8721/21291|2907/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8721C>T|p.Asp2907Asp|8721/13218|8721/13218|2907/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.432C>T|p.Asp144Asp|432/1500|432/1500|144/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.432C>T|p.Asp144Asp|432/1500|432/1500|144/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1069C>T|||||1069|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1069C>T|||||1069|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1987C>T|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1987C>T|||||1987|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2857C>T|||||2857|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2857C>T|||||2857|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3106C>T|||||3106|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3106C>T|||||3106|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3700C>T|||||3700|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3700C>T|||||3700|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-4039C>T|||||4039|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-4039C>T|||||4039|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4456C>T|||||4456|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4456C>T|||||4456|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*432C>T|||||432|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*432C>T|||||432|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:920:114,804:114:3988:804:28119:-2078.41,0,-73.1119
NC_045512.2	9026	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=71;CIGAR=1X;DP=1113;DPB=1113;DPRA=0;EPP=3.04088;EPPR=4.01893;GTI=0;LEN=1;MEANALT=1;MQM=41.831;MQMR=49.8301;NS=1;NUMALT=1;ODDS=885.288;PAIRED=1;PAIREDR=0.997121;PAO=0;PQA=0;PQR=0;PRO=0;QA=2421;QR=36529;RO=1042;RPL=33;RPP=3.7749;RPPR=21.4241;RPR=38;RUN=1;SAF=36;SAP=3.04088;SAR=35;SRF=532;SRP=4.01893;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8761A>T|p.Ile2921Phe|8761/21291|8761/21291|2921/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8761A>T|p.Ile2921Phe|8761/13218|8761/13218|2921/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.472A>T|p.Ile158Phe|472/1500|472/1500|158/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.472A>T|p.Ile158Phe|472/1500|472/1500|158/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1029A>T|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1029A>T|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1947A>T|||||1947|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1947A>T|||||1947|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2817A>T|||||2817|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2817A>T|||||2817|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3066A>T|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3066A>T|||||3066|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3660A>T|||||3660|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3660A>T|||||3660|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3999A>T|||||3999|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3999A>T|||||3999|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4416A>T|||||4416|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4416A>T|||||4416|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*472A>T|||||472|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*472A>T|||||472|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1113:1042,71:1042:36529:71:2421:0,-157.653,-2908.65
NC_045512.2	9053	.	G	T	22309.4	.	AB=0.843808;ABP=1113.91;AC=1;AF=0.5;AN=2;AO=913;CIGAR=1X;DP=1082;DPB=1082;DPRA=0;EPP=3.06976;EPPR=3.12594;GTI=0;LEN=1;MEANALT=1;MQM=49.3527;MQMR=52.2071;NS=1;NUMALT=1;ODDS=124.118;PAIRED=0.996714;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=32053;QR=5942;RO=169;RPL=427;RPP=11.2895;RPPR=17.0028;RPR=486;RUN=1;SAF=458;SAP=3.03171;SAR=455;SRF=84;SRP=3.02315;SRR=85;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8788G>T|p.Val2930Leu|8788/21291|8788/21291|2930/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8788G>T|p.Val2930Leu|8788/13218|8788/13218|2930/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.499G>T|p.Val167Leu|499/1500|499/1500|167/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.499G>T|p.Val167Leu|499/1500|499/1500|167/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-1002G>T|||||1002|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-1002G>T|||||1002|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1920G>T|||||1920|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1920G>T|||||1920|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2790G>T|||||2790|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2790G>T|||||2790|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-3039G>T|||||3039|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-3039G>T|||||3039|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3633G>T|||||3633|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3633G>T|||||3633|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3972G>T|||||3972|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3972G>T|||||3972|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4389G>T|||||4389|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4389G>T|||||4389|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*499G>T|||||499|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*499G>T|||||499|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1082:169,913:169:5942:913:32053:-2362.09,0,-184.534
NC_045512.2	9241	.	A	T	1.11862E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1557;DPB=1557;DPRA=0;EPP=4.31318;EPPR=9.9256;GTI=0;LEN=1;MEANALT=2;MQM=47.4833;MQMR=49.9773;NS=1;NUMALT=1;ODDS=1548.51;PAIRED=0.966667;PAIREDR=0.968562;PAO=0;PQA=0;PQR=0;PRO=0;QA=2105;QR=52635;RO=1495;RPL=6;RPP=86.3948;RPPR=275.336;RPR=54;RUN=1;SAF=33;SAP=4.31318;SAR=27;SRF=749;SRP=3.02337;SRR=746;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.8976A>T|p.Ser2992Ser|8976/21291|8976/21291|2992/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.8976A>T|p.Ser2992Ser|8976/13218|8976/13218|2992/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.687A>T|p.Ser229Ser|687/1500|687/1500|229/499||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.687A>T|p.Ser229Ser|687/1500|687/1500|229/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-814A>T|||||814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-814A>T|||||814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1732A>T|||||1732|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1732A>T|||||1732|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2602A>T|||||2602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2602A>T|||||2602|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2851A>T|||||2851|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2851A>T|||||2851|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3445A>T|||||3445|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3445A>T|||||3445|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3784A>T|||||3784|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3784A>T|||||3784|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-4201A>T|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-4201A>T|||||4201|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*687A>T|||||687|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*687A>T|||||687|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1557:1495,60:1495:52635:60:2105:0,-298.895,-4239.78
NC_045512.2	9445	.	T	C	2.15045E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=91;CIGAR=1X;DP=1927;DPB=1927;DPRA=0;EPP=3.22506;EPPR=3.12857;GTI=0;LEN=1;MEANALT=1;MQM=49.0769;MQMR=50.7925;NS=1;NUMALT=1;ODDS=1726.32;PAIRED=1;PAIREDR=0.961329;PAO=0;PQA=0;PQR=0;PRO=0;QA=3146;QR=64355;RO=1836;RPL=56;RPP=13.5336;RPPR=8.16222;RPR=35;RUN=1;SAF=44;SAP=3.22506;SAR=47;SRF=896;SRP=5.30004;SRR=940;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9180T>C|p.Leu3060Leu|9180/21291|9180/21291|3060/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9180T>C|p.Leu3060Leu|9180/13218|9180/13218|3060/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.891T>C|p.Leu297Leu|891/1500|891/1500|297/499||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.891T>C|p.Leu297Leu|891/1500|891/1500|297/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-610T>C|||||610|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-610T>C|||||610|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1528T>C|||||1528|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1528T>C|||||1528|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2398T>C|||||2398|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2398T>C|||||2398|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2647T>C|||||2647|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2647T>C|||||2647|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3241T>C|||||3241|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3241T>C|||||3241|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3580T>C|||||3580|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3580T>C|||||3580|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3997T>C|||||3997|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3997T>C|||||3997|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*891T>C|||||891|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*891T>C|||||891|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1927:1836,91:1836:64355:91:3146:0,-321.171,-5169.55
NC_045512.2	9511	.	T	C	4.64324E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=220;CIGAR=1X;DP=2576;DPB=2576;DPRA=0;EPP=3.16823;EPPR=19.815;GTI=0;LEN=1;MEANALT=2;MQM=48.6909;MQMR=51.9338;NS=1;NUMALT=1;ODDS=1399.05;PAIRED=0.986364;PAIREDR=0.990658;PAO=0;PQA=0;PQR=0;PRO=0;QA=7616;QR=83328;RO=2355;RPL=124;RPP=10.7486;RPPR=413.229;RPR=96;RUN=1;SAF=108;SAP=3.16823;SAR=112;SRF=1215;SRP=8.19694;SRR=1140;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9246T>C|p.Thr3082Thr|9246/21291|9246/21291|3082/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9246T>C|p.Thr3082Thr|9246/13218|9246/13218|3082/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.957T>C|p.Thr319Thr|957/1500|957/1500|319/499||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.957T>C|p.Thr319Thr|957/1500|957/1500|319/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-544T>C|||||544|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-544T>C|||||544|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1462T>C|||||1462|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1462T>C|||||1462|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2332T>C|||||2332|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2332T>C|||||2332|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2581T>C|||||2581|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2581T>C|||||2581|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3175T>C|||||3175|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3175T>C|||||3175|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3514T>C|||||3514|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3514T>C|||||3514|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3931T>C|||||3931|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3931T>C|||||3931|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*957T>C|||||957|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*957T>C|||||957|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2576:2355,220:2355:83328:220:7616:0,-150.664,-6510.68
NC_045512.2	9521	.	C	T	5.11094E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=56;CIGAR=1X;DP=2683;DPB=2683;DPRA=0;EPP=3.63072;EPPR=12.4812;GTI=0;LEN=1;MEANALT=2;MQM=42.4643;MQMR=51.472;NS=1;NUMALT=1;ODDS=3128.98;PAIRED=0.946429;PAIREDR=0.992762;PAO=0;PQA=0;PQR=0;PRO=0;QA=1974;QR=91769;RO=2625;RPL=11;RPP=47.8357;RPPR=156.677;RPR=45;RUN=1;SAF=29;SAP=3.16541;SAR=27;SRF=1329;SRP=3.91115;SRR=1296;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9256C>T|p.Leu3086Phe|9256/21291|9256/21291|3086/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9256C>T|p.Leu3086Phe|9256/13218|9256/13218|3086/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.967C>T|p.Leu323Phe|967/1500|967/1500|323/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.967C>T|p.Leu323Phe|967/1500|967/1500|323/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-534C>T|||||534|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-534C>T|||||534|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1452C>T|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1452C>T|||||1452|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2322C>T|||||2322|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2322C>T|||||2322|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2571C>T|||||2571|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2571C>T|||||2571|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3165C>T|||||3165|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3165C>T|||||3165|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3504C>T|||||3504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3504C>T|||||3504|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3921C>T|||||3921|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3921C>T|||||3921|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2683:2625,56:2625:91769:56:1974:0,-659.011,-7674.21
NC_045512.2	9627	.	CTTTTTTAG	CTTTTTAG	3.32693E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1M1D7M;DP=2471;DPB=2468.56;DPRA=0;EPP=3.29983;EPPR=8.18457;GTI=0;LEN=1;MEANALT=11;MQM=48.4667;MQMR=52.5949;NS=1;NUMALT=1;ODDS=3061.58;PAIRED=1;PAIREDR=0.987624;PAO=1.5;PQA=40;PQR=40;PRO=1.5;QA=944;QR=85133;RO=2424;RPL=17;RPP=4.16842;RPPR=20.5684;RPR=13;RUN=1;SAF=15;SAP=3.0103;SAR=15;SRF=1234;SRP=4.74461;SRR=1190;TYPE=del;ANN=CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9368delT|p.Leu3123fs|9368/21291|9368/21291|3123/7096||,CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9368delT|p.Leu3123fs|9368/13218|9368/13218|3123/4405||,CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1079delT|p.Leu360fs|1079/1500|1079/1500|360/499||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1079delT|p.Leu360fs|1079/1500|1079/1500|360/499||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-422delT|||||422|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-422delT|||||422|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1340delT|||||1340|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1340delT|||||1340|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2210delT|||||2210|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2210delT|||||2210|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2459delT|||||2459|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2459delT|||||2459|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-3053delT|||||3053|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-3053delT|||||3053|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3392delT|||||3392|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3392delT|||||3392|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3809delT|||||3809|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3809delT|||||3809|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1079delT|||||1079|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1079delT|||||1079|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2471:2424,30:2424:85133:30:944:0,-655.432,-7265.75
NC_045512.2	9734	.	T	C	10284.7	.	AB=0.267343;ABP=1161.96;AC=1;AF=0.5;AN=2;AO=659;CIGAR=1X;DP=2465;DPB=2465;DPRA=0;EPP=3.09268;EPPR=4.65908;GTI=0;LEN=1;MEANALT=2;MQM=49.393;MQMR=51.5042;NS=1;NUMALT=1;ODDS=2368.13;PAIRED=1;PAIREDR=0.993344;PAO=0;PQA=0;PQR=0;PRO=0;QA=22831;QR=63717;RO=1803;RPL=324;RPP=3.40901;RPPR=35.0091;RPR=335;RUN=1;SAF=327;SAP=3.09268;SAR=332;SRF=892;SRP=3.44508;SRR=911;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9469T>C|p.Phe3157Leu|9469/21291|9469/21291|3157/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9469T>C|p.Phe3157Leu|9469/13218|9469/13218|3157/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1180T>C|p.Phe394Leu|1180/1500|1180/1500|394/499||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1180T>C|p.Phe394Leu|1180/1500|1180/1500|394/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-321T>C|||||321|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-321T>C|||||321|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1239T>C|||||1239|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1239T>C|||||1239|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-2109T>C|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-2109T>C|||||2109|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2358T>C|||||2358|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2358T>C|||||2358|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2952T>C|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2952T>C|||||2952|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3291T>C|||||3291|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3291T>C|||||3291|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3708T>C|||||3708|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3708T>C|||||3708|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1180T>C|||||1180|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1180T>C|||||1180|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2465:1803,659:1803:63717:659:22831:-1156.78,0,-4685.13
NC_045512.2	9865	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=945;DPB=945;DPRA=0;EPP=3.20771;EPPR=4.13556;GTI=0;LEN=1;MEANALT=1;MQM=50.3636;MQMR=51.8437;NS=1;NUMALT=1;ODDS=1188.97;PAIRED=0.909091;PAIREDR=0.981799;PAO=0;PQA=0;PQR=0;PRO=0;QA=377;QR=32898;RO=934;RPL=4;RPP=4.78696;RPPR=16.439;RPR=7;RUN=1;SAF=6;SAP=3.20771;SAR=5;SRF=483;SRP=5.39101;SRR=451;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9600T>C|p.Pro3200Pro|9600/21291|9600/21291|3200/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9600T>C|p.Pro3200Pro|9600/13218|9600/13218|3200/4405||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1311T>C|p.Pro437Pro|1311/1500|1311/1500|437/499||WARNING_TRANSCRIPT_NO_START_CODON,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1311T>C|p.Pro437Pro|1311/1500|1311/1500|437/499||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-190T>C|||||190|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-190T>C|||||190|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1108T>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1108T>C|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1978T>C|||||1978|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1978T>C|||||1978|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2227T>C|||||2227|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2227T>C|||||2227|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2821T>C|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2821T>C|||||2821|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3160T>C|||||3160|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3160T>C|||||3160|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3577T>C|||||3577|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3577T>C|||||3577|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1311T>C|||||1311|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1311T>C|||||1311|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:945:934,11:934:32898:11:377:0,-252.906,-2775.77
NC_045512.2	9891	.	C	T	7564.06	.	AB=0.350235;ABP=210.495;AC=1;AF=0.5;AN=2;AO=373;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.99416;EPPR=4.97437;GTI=0;LEN=1;MEANALT=2;MQM=50.5684;MQMR=52.7902;NS=1;NUMALT=1;ODDS=1741.69;PAIRED=0.994638;PAIREDR=0.984081;PAO=0;PQA=0;PQR=0;PRO=0;QA=13059;QR=24218;RO=691;RPL=182;RPP=3.48185;RPPR=6.43249;RPR=191;RUN=1;SAF=188;SAP=3.06269;SAR=185;SRF=347;SRP=3.03858;SRR=344;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9626C>T|p.Ala3209Val|9626/21291|9626/21291|3209/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9626C>T|p.Ala3209Val|9626/13218|9626/13218|3209/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1337C>T|p.Ala446Val|1337/1500|1337/1500|446/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1337C>T|p.Ala446Val|1337/1500|1337/1500|446/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-164C>T|||||164|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-164C>T|||||164|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-1082C>T|||||1082|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-1082C>T|||||1082|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1952C>T|||||1952|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1952C>T|||||1952|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2201C>T|||||2201|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2201C>T|||||2201|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2795C>T|||||2795|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2795C>T|||||2795|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-3134C>T|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-3134C>T|||||3134|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3551C>T|||||3551|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3551C>T|||||3551|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1337C>T|||||1337|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1337C>T|||||1337|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1065:691,373:691:24218:373:13059:-785.258,0,-1781.24
NC_045512.2	10029	.	C	T	9917.01	.	AB=0.509918;ABP=3.74257;AC=1;AF=0.5;AN=2;AO=437;CIGAR=1X;DP=857;DPB=857;DPRA=0;EPP=4.80412;EPPR=3.01548;GTI=0;LEN=1;MEANALT=2;MQM=48.9451;MQMR=53.5131;NS=1;NUMALT=1;ODDS=2283.48;PAIRED=0.990847;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=15164;QR=14518;RO=419;RPL=203;RPP=7.78555;RPPR=4.17637;RPR=234;RUN=1;SAF=216;SAP=3.13453;SAR=221;SRF=209;SRP=3.01548;SRR=210;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9764C>T|p.Thr3255Ile|9764/21291|9764/21291|3255/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9764C>T|p.Thr3255Ile|9764/13218|9764/13218|3255/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding|1/1|c.1475C>T|p.Thr492Ile|1475/1500|1475/1500|492/499||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding|1/1|c.1475C>T|p.Thr492Ile|1475/1500|1475/1500|492/499||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.-26C>T|||||26|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.-26C>T|||||26|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-944C>T|||||944|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-944C>T|||||944|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1814C>T|||||1814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1814C>T|||||1814|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-2063C>T|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-2063C>T|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2657C>T|||||2657|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2657C>T|||||2657|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2996C>T|||||2996|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2996C>T|||||2996|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3413C>T|||||3413|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3413C>T|||||3413|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1475C>T|||||1475|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1475C>T|||||1475|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:857:419,437:419:14518:437:15164:-1000.27,0,-1019.67
NC_045512.2	10228	.	C	T	13986.5	.	AB=0.280464;ABP=1267.26;AC=1;AF=0.5;AN=2;AO=847;CIGAR=1X;DP=3020;DPB=3020;DPRA=0;EPP=3.01286;EPPR=3.58669;GTI=0;LEN=1;MEANALT=3;MQM=49.3318;MQMR=52.8512;NS=1;NUMALT=1;ODDS=3220.5;PAIRED=0.995277;PAIREDR=0.99447;PAO=0;PQA=0;PQR=0;PRO=0;QA=29649;QR=76244;RO=2170;RPL=439;RPP=5.47404;RPPR=3.07434;RPR=408;RUN=1;SAF=423;SAP=3.01286;SAR=424;SRF=1084;SRP=3.0143;SRR=1086;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.9963C>T|p.Leu3321Leu|9963/21291|9963/21291|3321/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.9963C>T|p.Leu3321Leu|9963/13218|9963/13218|3321/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.174C>T|p.Leu58Leu|174/918|174/918|58/305||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.174C>T|p.Leu58Leu|174/918|174/918|58/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-745C>T|||||745|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-745C>T|||||745|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1615C>T|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1615C>T|||||1615|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1864C>T|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1864C>T|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2458C>T|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2458C>T|||||2458|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2797C>T|||||2797|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2797C>T|||||2797|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3214C>T|||||3214|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3214C>T|||||3214|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1674C>T|||||1674|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1674C>T|||||1674|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*174C>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*174C>T|||||174|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3020:2170,847:2170:76244:847:29649:-1537.73,0,-5713.37
NC_045512.2	10408	.	C	T	7069.66	.	AB=0.250962;ABP=1263.03;AC=1;AF=0.5;AN=2;AO=587;CIGAR=1X;DP=2339;DPB=2339;DPRA=0;EPP=3.30994;EPPR=4.99565;GTI=0;LEN=1;MEANALT=2;MQM=45.0187;MQMR=51.1657;NS=1;NUMALT=1;ODDS=1627.85;PAIRED=0.945486;PAIREDR=0.993714;PAO=0;PQA=0;PQR=0;PRO=0;QA=20801;QR=61151;RO=1750;RPL=466;RPP=443.316;RPPR=97.5326;RPR=121;RUN=1;SAF=290;SAP=3.19156;SAR=297;SRF=870;SRP=3.13438;SRR=880;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10143C>T|p.Tyr3381Tyr|10143/21291|10143/21291|3381/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10143C>T|p.Tyr3381Tyr|10143/13218|10143/13218|3381/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.354C>T|p.Tyr118Tyr|354/918|354/918|118/305||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.354C>T|p.Tyr118Tyr|354/918|354/918|118/305||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-565C>T|||||565|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1435C>T|||||1435|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1435C>T|||||1435|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1684C>T|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1684C>T|||||1684|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2278C>T|||||2278|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2278C>T|||||2278|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2617C>T|||||2617|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2617C>T|||||2617|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-3034C>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-3034C>T|||||3034|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1854C>T|||||1854|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1854C>T|||||1854|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*354C>T|||||354|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*354C>T|||||354|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2339:1750,587:1750:61151:587:20801:-893.549,0,-4490.38
NC_045512.2	10487	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=60;CIGAR=1X;DP=1268;DPB=1268;DPRA=0;EPP=3.15506;EPPR=4.85102;GTI=0;LEN=1;MEANALT=1;MQM=50.7;MQMR=52.9139;NS=1;NUMALT=1;ODDS=1130.67;PAIRED=1;PAIREDR=0.990066;PAO=0;PQA=0;PQR=0;PRO=0;QA=2080;QR=42478;RO=1208;RPL=27;RPP=4.31318;RPPR=45.6416;RPR=33;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=611;SRP=3.36262;SRR=597;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10222T>C|p.Cys3408Arg|10222/21291|10222/21291|3408/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10222T>C|p.Cys3408Arg|10222/13218|10222/13218|3408/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding|1/1|c.433T>C|p.Cys145Arg|433/918|433/918|145/305||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding|1/1|c.433T>C|p.Cys145Arg|433/918|433/918|145/305||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.-486T>C|||||486|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.-486T>C|||||486|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-1356T>C|||||1356|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-1356T>C|||||1356|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1605T>C|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1605T>C|||||1605|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-2199T>C|||||2199|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-2199T>C|||||2199|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-2538T>C|||||2538|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-2538T>C|||||2538|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2955T>C|||||2955|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2955T>C|||||2955|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*1933T>C|||||1933|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*1933T>C|||||1933|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*433T>C|||||433|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*433T>C|||||433|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1268:1208,60:1208:42478:60:2080:0,-207.823,-3511.98
NC_045512.2	11074	.	CTTTTTTTTGTATGA	CTTTTTTTGTATGA,CTTTTTTTTTGTATGA	4.6288E-14	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=13,12;CIGAR=1M1D13M,1M1I14M;DP=552;DPB=552;DPRA=0,0;EPP=3.17734,3.0103;EPPR=3.07737;GTI=0;LEN=1,1;MEANALT=9,9;MQM=54,48.9167;MQMR=49.0734;NS=1;NUMALT=2;ODDS=598.293;PAIRED=0.923077,0.833333;PAIREDR=0.878378;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=433,386;QR=17910;RO=518;RPL=4,6;RPP=7.18621,3.0103;RPPR=209.61;RPR=9,6;RUN=1,1;SAF=6,6;SAP=3.17734,3.0103;SAR=7,6;SRF=273;SRP=6.29685;SRR=245;TYPE=del,ins;ANN=CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817delT|p.Leu3606fs|10817/21291|10817/21291|3606/7096||,CTTTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10817dupT|p.Leu3606fs|10818/21291|10818/21291|3606/7096||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817delT|p.Leu3606fs|10817/13218|10817/13218|3606/4405||,CTTTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10817dupT|p.Leu3606fs|10818/13218|10818/13218|3606/4405||,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110delT|p.Leu37fs|110/870|110/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.110dupT|p.Leu37fs|111/870|111/870|37/289||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-761dupT|||||760|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-761delT|||||761|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-761dupT|||||760|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-1010dupT|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1010delT|||||1010|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-1010dupT|||||1009|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1604dupT|||||1603|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1604delT|||||1604|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1604dupT|||||1603|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1943dupT|||||1942|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1943delT|||||1943|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1943dupT|||||1942|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2360dupT|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2360delT|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2360dupT|||||2359|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2528dupT|||||2529|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2528delT|||||2528|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2528dupT|||||2529|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1028dupT|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1028delT|||||1028|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1028dupT|||||1029|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*110dupT|||||111|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*110delT|||||110|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTTTTTGTATGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*110dupT|||||111|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.14)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:552:518,13,12:518:17910:13,12:433,386:0,-121.139,-1418.29,-125.159,-1391.45,-1422.6
NC_045512.2	11151	.	T	A	9.76452E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=800;DPB=800;DPRA=0;EPP=3.73412;EPPR=3.40712;GTI=0;LEN=1;MEANALT=1;MQM=42.8333;MQMR=53.0863;NS=1;NUMALT=1;ODDS=993.402;PAIRED=0.5;PAIREDR=0.984772;PAO=0;PQA=0;PQR=0;PRO=0;QA=375;QR=27325;RO=788;RPL=2;RPP=14.5915;RPPR=3.55041;RPR=10;RUN=1;SAF=7;SAP=3.73412;SAR=5;SRF=403;SRP=3.90314;SRR=385;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10886T>A|p.Val3629Asp|10886/21291|10886/21291|3629/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10886T>A|p.Val3629Asp|10886/13218|10886/13218|3629/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.179T>A|p.Val60Asp|179/870|179/870|60/289||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.179T>A|p.Val60Asp|179/870|179/870|60/289||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-692T>A|||||692|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-692T>A|||||692|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-941T>A|||||941|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-941T>A|||||941|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1535T>A|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1535T>A|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1874T>A|||||1874|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1874T>A|||||1874|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2291T>A|||||2291|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2291T>A|||||2291|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2597T>A|||||2597|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2597T>A|||||2597|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1097T>A|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1097T>A|||||1097|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*179T>A|||||179|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*179T>A|||||179|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:800:788,12:788:27325:12:375:0,-211.506,-2350.92
NC_045512.2	11201	.	A	G	19964.4	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1X;DP=801;DPB=801;DPRA=0;EPP=8.6608;EPPR=3.16541;GTI=0;LEN=1;MEANALT=2;MQM=52.1452;MQMR=55.5179;NS=1;NUMALT=1;ODDS=516.482;PAIRED=0.978495;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=25349;QR=1957;RO=56;RPL=371;RPP=3.02197;RPPR=4.40625;RPR=373;RUN=1;SAF=363;SAP=3.95594;SAR=381;SRF=28;SRP=3.0103;SRR=28;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.10936A>G|p.Thr3646Ala|10936/21291|10936/21291|3646/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.10936A>G|p.Thr3646Ala|10936/13218|10936/13218|3646/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.229A>G|p.Thr77Ala|229/870|229/870|77/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.229A>G|p.Thr77Ala|229/870|229/870|77/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-642A>G|||||642|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-642A>G|||||642|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-891A>G|||||891|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-891A>G|||||891|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1485A>G|||||1485|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1485A>G|||||1485|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1824A>G|||||1824|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1824A>G|||||1824|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2241A>G|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2241A>G|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2647A>G|||||2647|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2647A>G|||||2647|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1147A>G|||||1147|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1147A>G|||||1147|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*229A>G|||||229|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*229A>G|||||229|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:801:56,744:56:1957:744:25349:-1998.63,-65.2713,0
NC_045512.2	11332	.	A	G	18029.6	.	AB=0.54144;ABP=24.967;AC=1;AF=0.5;AN=2;AO=797;CIGAR=1X;DP=1472;DPB=1472;DPRA=0;EPP=11.2521;EPPR=6.73467;GTI=0;LEN=1;MEANALT=2;MQM=48.9849;MQMR=50.908;NS=1;NUMALT=1;ODDS=3264.3;PAIRED=0.991217;PAIREDR=0.991098;PAO=0;PQA=0;PQR=0;PRO=0;QA=27379;QR=23660;RO=674;RPL=287;RPP=138.5;RPPR=1116.92;RPR=510;RUN=1;SAF=397;SAP=3.03482;SAR=400;SRF=351;SRP=5.53617;SRR=323;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11067A>G|p.Val3689Val|11067/21291|11067/21291|3689/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11067A>G|p.Val3689Val|11067/13218|11067/13218|3689/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.360A>G|p.Val120Val|360/870|360/870|120/289||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.360A>G|p.Val120Val|360/870|360/870|120/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-511A>G|||||511|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-511A>G|||||511|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-760A>G|||||760|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-760A>G|||||760|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1354A>G|||||1354|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1354A>G|||||1354|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1693A>G|||||1693|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1693A>G|||||1693|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2110A>G|||||2110|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2110A>G|||||2110|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4905A>G|||||4905|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2778A>G|||||2778|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2778A>G|||||2778|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1278A>G|||||1278|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1278A>G|||||1278|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*360A>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*360A>G|||||360|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1472:674,797:674:23660:797:27379:-1828.07,0,-1561.87
NC_045512.2	11418	.	T	C	1582.81	.	AB=0.162816;ABP=2695.99;AC=1;AF=0.5;AN=2;AO=444;CIGAR=1X;DP=2727;DPB=2727;DPRA=0;EPP=3.08855;EPPR=9.28929;GTI=0;LEN=1;MEANALT=3;MQM=49.1554;MQMR=52.3698;NS=1;NUMALT=1;ODDS=364.456;PAIRED=0.984234;PAIREDR=0.990745;PAO=0;PQA=0;PQR=0;PRO=0;QA=15540;QR=78990;RO=2269;RPL=231;RPP=4.59489;RPPR=4.94826;RPR=213;RUN=1;SAF=227;SAP=3.49937;SAR=217;SRF=1153;SRP=4.32046;SRR=1116;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11153T>C|p.Val3718Ala|11153/21291|11153/21291|3718/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11153T>C|p.Val3718Ala|11153/13218|11153/13218|3718/4405||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.446T>C|p.Val149Ala|446/870|446/870|149/289||WARNING_TRANSCRIPT_NO_START_CODON,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.446T>C|p.Val149Ala|446/870|446/870|149/289||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-425T>C|||||425|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-425T>C|||||425|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-674T>C|||||674|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-674T>C|||||674|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1268T>C|||||1268|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1268T>C|||||1268|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1607T>C|||||1607|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1607T>C|||||1607|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-2024T>C|||||2024|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-2024T>C|||||2024|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4819T>C|||||4819|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2864T>C|||||2864|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2864T>C|||||2864|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1364T>C|||||1364|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1364T>C|||||1364|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*446T>C|||||446|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*446T>C|||||446|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2727:2269,444:2269:78990:444:15540:-458.018,0,-6000.58
NC_045512.2	11514	.	C	T	1173.47	.	AB=0.159434;ABP=2208.29;AC=1;AF=0.5;AN=2;AO=349;CIGAR=1X;DP=2189;DPB=2189;DPRA=0;EPP=3.01652;EPPR=3.03982;GTI=0;LEN=1;MEANALT=2;MQM=49.7536;MQMR=50.8967;NS=1;NUMALT=1;ODDS=270.201;PAIRED=0.988539;PAIREDR=0.990212;PAO=0;PQA=0;PQR=0;PRO=0;QA=12248;QR=64514;RO=1839;RPL=205;RPP=26.1623;RPPR=43.4228;RPR=144;RUN=1;SAF=175;SAP=3.01652;SAR=174;SRF=924;SRP=3.10594;SRR=915;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11249C>T|p.Thr3750Ile|11249/21291|11249/21291|3750/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11249C>T|p.Thr3750Ile|11249/13218|11249/13218|3750/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.542C>T|p.Thr181Ile|542/870|542/870|181/289||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.542C>T|p.Thr181Ile|542/870|542/870|181/289||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-329C>T|||||329|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-329C>T|||||329|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-578C>T|||||578|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-578C>T|||||578|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1172C>T|||||1172|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1172C>T|||||1172|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1511C>T|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1511C>T|||||1511|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1928C>T|||||1928|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1928C>T|||||1928|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4723C>T|||||4723|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2960C>T|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2960C>T|||||2960|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1460C>T|||||1460|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1460C>T|||||1460|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*542C>T|||||542|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*542C>T|||||542|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2189:1839,349:1839:64514:349:12248:-369.053,0,-4782.23
NC_045512.2	11522	.	T	G	3.80427E-13	.	AB=0.132833;ABP=2656.4;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=2266;DPB=2266;DPRA=0;EPP=3.07523;EPPR=3.19725;GTI=0;LEN=1;MEANALT=2;MQM=49.5449;MQMR=51.4249;NS=1;NUMALT=1;ODDS=255.329;PAIRED=0.993355;PAIREDR=0.987264;PAO=0;PQA=0;PQR=0;PRO=0;QA=10440;QR=68620;RO=1963;RPL=176;RPP=21.7744;RPPR=13.4185;RPR=125;RUN=1;SAF=150;SAP=3.01751;SAR=151;SRF=989;SRP=3.2592;SRR=974;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11257T>G|p.Phe3753Val|11257/21291|11257/21291|3753/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11257T>G|p.Phe3753Val|11257/13218|11257/13218|3753/4405||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.550T>G|p.Phe184Val|550/870|550/870|184/289||WARNING_TRANSCRIPT_NO_START_CODON,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.550T>G|p.Phe184Val|550/870|550/870|184/289||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-321T>G|||||321|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-321T>G|||||321|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-570T>G|||||570|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-570T>G|||||570|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1164T>G|||||1164|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1164T>G|||||1164|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1503T>G|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1503T>G|||||1503|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1920T>G|||||1920|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1920T>G|||||1920|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4715T>G|||||4715|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*2968T>G|||||2968|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*2968T>G|||||2968|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1468T>G|||||1468|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1468T>G|||||1468|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*550T>G|||||550|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*550T>G|||||550|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2266:1963,301:1963:68620:301:10440:-194.762,0,-5142.94
NC_045512.2	11593	.	TC	GA	1.75387E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=2X;DP=2530;DPB=2530;DPRA=0;EPP=3.08035;EPPR=4.33407;GTI=0;LEN=2;MEANALT=3;MQM=42.6452;MQMR=52.4405;NS=1;NUMALT=1;ODDS=3169.29;PAIRED=0.83871;PAIREDR=0.990381;PAO=0;PQA=0;PQR=0;PRO=0;QA=1093;QR=87869;RO=2495;RPL=7;RPP=23.254;RPPR=103.029;RPR=24;RUN=1;SAF=14;SAP=3.64073;SAR=17;SRF=1238;SRP=3.32449;SRR=1257;TYPE=complex;ANN=GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11328_11329delTCinsGA|p.Gln3777Lys|11328/21291|11328/21291|3776/7096||,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11328_11329delTCinsGA|p.Gln3777Lys|11328/13218|11328/13218|3776/4405||,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding|1/1|c.621_622delTCinsGA|p.Gln208Lys|621/870|621/870|207/289||WARNING_TRANSCRIPT_NO_START_CODON,GA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding|1/1|c.621_622delTCinsGA|p.Gln208Lys|621/870|621/870|207/289||WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.-250_-249delTCinsGA|||||250|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.-250_-249delTCinsGA|||||250|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-499_-498delTCinsGA|||||499|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-499_-498delTCinsGA|||||499|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-1093_-1092delTCinsGA|||||1093|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-1093_-1092delTCinsGA|||||1093|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1432_-1431delTCinsGA|||||1432|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1432_-1431delTCinsGA|||||1432|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1849_-1848delTCinsGA|||||1849|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1849_-1848delTCinsGA|||||1849|WARNING_TRANSCRIPT_NO_START_CODON,GA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4644_-4643delTCinsGA|||||4644|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3039_*3040delTCinsGA|||||3039|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3039_*3040delTCinsGA|||||3039|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1539_*1540delTCinsGA|||||1539|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1539_*1540delTCinsGA|||||1539|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*621_*622delTCinsGA|||||621|WARNING_TRANSCRIPT_NO_START_CODON,GA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*621_*622delTCinsGA|||||621|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2530:2495,31:2495:87869:31:1093:0,-680.809,-7515.53
NC_045512.2	11952	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.87889;EPPR=17.5825;GTI=0;LEN=1;MEANALT=1;MQM=37.075;MQMR=52.3812;NS=1;NUMALT=1;ODDS=4814.2;PAIRED=1;PAIREDR=0.988441;PAO=0;PQA=0;PQR=0;PRO=0;QA=1331;QR=131082;RO=3720;RPL=2;RPP=73.366;RPPR=302.263;RPR=38;RUN=1;SAF=20;SAP=3.0103;SAR=20;SRF=1889;SRP=4.97396;SRR=1831;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11687A>T|p.Asn3896Ile|11687/21291|11687/21291|3896/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11687A>T|p.Asn3896Ile|11687/13218|11687/13218|3896/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding|1/1|c.110A>T|p.Asn37Ile|110/249|110/249|37/82||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding|1/1|c.110A>T|p.Asn37Ile|110/249|110/249|37/82||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.-140A>T|||||140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.-140A>T|||||140|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-734A>T|||||734|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-734A>T|||||734|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-1073A>T|||||1073|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-1073A>T|||||1073|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1490A>T|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1490A>T|||||1490|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4285A>T|||||4285|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3398A>T|||||3398|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3398A>T|||||3398|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*1898A>T|||||1898|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*1898A>T|||||1898|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*980A>T|||||980|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*980A>T|||||980|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*110A>T|||||110|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*110A>T|||||110|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3760:3720,40:3720:131082:40:1331:0,-1040.87,-11225.6
NC_045512.2	12165	.	C	T	7.43742E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=48;CIGAR=1X;DP=4731;DPB=4731;DPRA=0;EPP=3.0103;EPPR=5.62303;GTI=0;LEN=1;MEANALT=3;MQM=48.1042;MQMR=52.3067;NS=1;NUMALT=1;ODDS=5980.48;PAIRED=1;PAIREDR=0.995722;PAO=0;PQA=0;PQR=0;PRO=0;QA=1663;QR=163625;RO=4675;RPL=31;RPP=11.8771;RPPR=191.484;RPR=17;RUN=1;SAF=23;SAP=3.19126;SAR=25;SRF=2325;SRP=3.3006;SRR=2350;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.11900C>T|p.Ala3967Val|11900/21291|11900/21291|3967/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.11900C>T|p.Ala3967Val|11900/13218|11900/13218|3967/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.74C>T|p.Ala25Val|74/594|74/594|25/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.74C>T|p.Ala25Val|74/594|74/594|25/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-521C>T|||||521|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-521C>T|||||521|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-860C>T|||||860|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-860C>T|||||860|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1277C>T|||||1277|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1277C>T|||||1277|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-4072C>T|||||4072|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3611C>T|||||3611|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3611C>T|||||3611|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2111C>T|||||2111|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2111C>T|||||2111|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1193C>T|||||1193|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1193C>T|||||1193|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*323C>T|||||323|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*323C>T|||||323|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*74C>T|||||74|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*74C>T|||||74|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4731:4675,48:4675:163625:48:1663:0,-1284.97,-13991
NC_045512.2	12395	.	G	A	4.42388E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=28;CIGAR=1X;DP=2722;DPB=2722;DPRA=0;EPP=3.0103;EPPR=8.70195;GTI=0;LEN=1;MEANALT=2;MQM=48.5714;MQMR=52.3105;NS=1;NUMALT=1;ODDS=3439.94;PAIRED=1;PAIREDR=0.995542;PAO=0;PQA=0;PQR=0;PRO=0;QA=1004;QR=93798;RO=2692;RPL=10;RPP=7.97367;RPPR=28.5679;RPR=18;RUN=1;SAF=14;SAP=3.0103;SAR=14;SRF=1323;SRP=4.71715;SRR=1369;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12130G>A|p.Ala4044Thr|12130/21291|12130/21291|4044/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12130G>A|p.Ala4044Thr|12130/13218|12130/13218|4044/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.304G>A|p.Ala102Thr|304/594|304/594|102/197||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.304G>A|p.Ala102Thr|304/594|304/594|102/197||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-291G>A|||||291|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-291G>A|||||291|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-630G>A|||||630|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-630G>A|||||630|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1047G>A|||||1047|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1047G>A|||||1047|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3842G>A|||||3842|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3841G>A|||||3841|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3841G>A|||||3841|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2341G>A|||||2341|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2341G>A|||||2341|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*553G>A|||||553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*553G>A|||||553|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*304G>A|||||304|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*304G>A|||||304|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2722:2692,28:2692:93798:28:1004:0,-736.807,-8035.4
NC_045512.2	12421	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=2716;DPB=2716;DPRA=0;EPP=3.0103;EPPR=7.0963;GTI=0;LEN=1;MEANALT=3;MQM=52;MQMR=51.0175;NS=1;NUMALT=1;ODDS=3350.88;PAIRED=1;PAIREDR=0.990668;PAO=0;PQA=0;PQR=0;PRO=0;QA=1216;QR=93869;RO=2679;RPL=26;RPP=23.7032;RPPR=139.93;RPR=8;RUN=1;SAF=17;SAP=3.0103;SAR=17;SRF=1326;SRP=3.60119;SRR=1353;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12156A>G|p.Ala4052Ala|12156/21291|12156/21291|4052/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12156A>G|p.Ala4052Ala|12156/13218|12156/13218|4052/4405||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.330A>G|p.Ala110Ala|330/594|330/594|110/197||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.330A>G|p.Ala110Ala|330/594|330/594|110/197||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-265A>G|||||265|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-265A>G|||||265|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-604A>G|||||604|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-604A>G|||||604|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-1021A>G|||||1021|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-1021A>G|||||1021|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3816A>G|||||3816|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3867A>G|||||3867|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3867A>G|||||3867|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2367A>G|||||2367|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2367A>G|||||2367|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1449A>G|||||1449|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1449A>G|||||1449|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*579A>G|||||579|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*579A>G|||||579|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*330A>G|||||330|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*330A>G|||||330|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2716:2679,34:2679:93869:34:1216:0,-710.041,-7872.24
NC_045512.2	12543	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=41;CIGAR=1X;DP=3019;DPB=3019;DPRA=0;EPP=3.06326;EPPR=8.53125;GTI=0;LEN=1;MEANALT=2;MQM=48.9756;MQMR=52.692;NS=1;NUMALT=1;ODDS=3704.8;PAIRED=0.95122;PAIREDR=0.993618;PAO=0;PQA=0;PQR=0;PRO=0;QA=1456;QR=104157;RO=2977;RPL=19;RPP=3.48696;RPPR=63.0916;RPR=22;RUN=1;SAF=22;SAP=3.48696;SAR=19;SRF=1517;SRP=5.38017;SRR=1460;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12278C>T|p.Ser4093Leu|12278/21291|12278/21291|4093/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12278C>T|p.Ser4093Leu|12278/13218|12278/13218|4093/4405||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding|1/1|c.452C>T|p.Ser151Leu|452/594|452/594|151/197||WARNING_TRANSCRIPT_NO_START_CODON,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding|1/1|c.452C>T|p.Ser151Leu|452/594|452/594|151/197||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.-143C>T|||||143|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.-143C>T|||||143|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.-482C>T|||||482|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.-482C>T|||||482|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-899C>T|||||899|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-899C>T|||||899|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3694C>T|||||3694|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*3989C>T|||||3989|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*3989C>T|||||3989|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*2489C>T|||||2489|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*2489C>T|||||2489|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*1571C>T|||||1571|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*1571C>T|||||1571|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*701C>T|||||701|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*701C>T|||||701|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*452C>T|||||452|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*452C>T|||||452|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3019:2977,41:2977:104157:41:1456:0,-788.671,-8910.43
NC_045512.2	13061	.	G	A	9.19732E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=53;CIGAR=1X;DP=3822;DPB=3822;DPRA=0;EPP=3.37904;EPPR=9.37237;GTI=0;LEN=1;MEANALT=3;MQM=49.0943;MQMR=50.8974;NS=1;NUMALT=1;ODDS=4686.48;PAIRED=1;PAIREDR=0.975817;PAO=0;PQA=0;PQR=0;PRO=0;QA=1858;QR=132219;RO=3763;RPL=45;RPP=59.0998;RPPR=63.9621;RPR=8;RUN=1;SAF=25;SAP=3.37904;SAR=28;SRF=1861;SRP=3.98034;SRR=1902;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12796G>A|p.Val4266Ile|12796/21291|12796/21291|4266/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12796G>A|p.Val4266Ile|12796/13218|12796/13218|4266/4405||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.37G>A|p.Val13Ile|37/417|37/417|13/138||WARNING_TRANSCRIPT_NO_START_CODON,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.37G>A|p.Val13Ile|37/417|37/417|13/138||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-381G>A|||||381|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-381G>A|||||381|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3176G>A|||||3176|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4979G>A|||||4979|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4507G>A|||||4507|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4507G>A|||||4507|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3007G>A|||||3007|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3007G>A|||||3007|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2089G>A|||||2089|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2089G>A|||||2089|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1219G>A|||||1219|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1219G>A|||||1219|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*970G>A|||||970|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*970G>A|||||970|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*376G>A|||||376|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*376G>A|||||376|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*37G>A|||||37|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*37G>A|||||37|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3822:3763,53:3763:132219:53:1858:0,-995.615,-11086.3
NC_045512.2	13105	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=105;CIGAR=1X;DP=3664;DPB=3664;DPRA=0;EPP=3.03098;EPPR=4.13971;GTI=0;LEN=1;MEANALT=3;MQM=48.1048;MQMR=51.373;NS=1;NUMALT=1;ODDS=3921.12;PAIRED=0.961905;PAIREDR=0.978059;PAO=0;PQA=0;PQR=0;PRO=0;QA=3675;QR=124917;RO=3555;RPL=50;RPP=3.52732;RPPR=26.2368;RPR=55;RUN=1;SAF=51;SAP=3.19643;SAR=54;SRF=1812;SRP=5.91842;SRR=1743;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12840C>T|p.Tyr4280Tyr|12840/21291|12840/21291|4280/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12840C>T|p.Tyr4280Tyr|12840/13218|12840/13218|4280/4405||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.81C>T|p.Tyr27Tyr|81/417|81/417|27/138||WARNING_TRANSCRIPT_NO_START_CODON,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.81C>T|p.Tyr27Tyr|81/417|81/417|27/138||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-337C>T|||||337|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-337C>T|||||337|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3132C>T|||||3132|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4935C>T|||||4935|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4551C>T|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4551C>T|||||4551|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3051C>T|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3051C>T|||||3051|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2133C>T|||||2133|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2133C>T|||||2133|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1263C>T|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1263C>T|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1014C>T|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1014C>T|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*420C>T|||||420|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*420C>T|||||420|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*81C>T|||||81|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*81C>T|||||81|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3664:3555,105:3555:124917:105:3675:0,-801.229,-10358.9
NC_045512.2	13162	.	TACACACACT	TACACACT	0.0	.	AB=0.112724;ABP=3863.02;AC=1;AF=0.5;AN=2;AO=334;CIGAR=1M2D7M;DP=2963;DPB=2897.9;DPRA=0;EPP=3.03631;EPPR=3.61938;GTI=0;LEN=2;MEANALT=21;MQM=50.9461;MQMR=53.5356;NS=1;NUMALT=1;ODDS=846.644;PAIRED=0.982036;PAIREDR=0.993844;PAO=3.5;PQA=96;PQR=96;PRO=3.5;QA=10732;QR=90583;RO=2599;RPL=178;RPP=6.15698;RPPR=30.3822;RPR=156;RUN=1;SAF=164;SAP=3.24435;SAR=170;SRF=1308;SRP=3.25176;SRR=1291;TYPE=del;ANN=TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|1/2|c.12904_12905delAC|p.Thr4302fs|12904/21291|12904/21291|4302/7096||,TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding|1/1|c.12904_12905delAC|p.Thr4302fs|12904/13218|12904/13218|4302/4405||,TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding|1/1|c.145_146delAC|p.Thr49fs|145/417|145/417|49/138||WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding|1/1|c.145_146delAC|p.Thr49fs|145/417|145/417|49/138||WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.-273_-272delAC|||||273|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.-273_-272delAC|||||273|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-3068_-3067delAC|||||3068|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4871_-4870delAC|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4615_*4616delAC|||||4615|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4615_*4616delAC|||||4615|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3115_*3116delAC|||||3115|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3115_*3116delAC|||||3115|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2197_*2198delAC|||||2197|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2197_*2198delAC|||||2197|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1327_*1328delAC|||||1327|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1327_*1328delAC|||||1327|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1078_*1079delAC|||||1078|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1078_*1079delAC|||||1078|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*484_*485delAC|||||484|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*484_*485delAC|||||484|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*145_*146delAC|||||145|WARNING_TRANSCRIPT_NO_START_CODON,TACACACT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*145_*146delAC|||||145|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.11)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2963:2599,334:2599:90583:334:10732:-71.6702,0,-7021.49
NC_045512.2	13514	.	G	A	4.65288E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=729;DPB=729;DPRA=0;EPP=3.0103;EPPR=3.15953;GTI=0;LEN=1;MEANALT=1;MQM=51.4375;MQMR=52.5203;NS=1;NUMALT=1;ODDS=839.999;PAIRED=1;PAIREDR=0.995792;PAO=0;PQA=0;PQR=0;PRO=0;QA=524;QR=24566;RO=713;RPL=6;RPP=5.18177;RPPR=53.6912;RPR=10;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=362;SRP=3.37881;SRR=351;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13250G>A|p.Gly4417Asp|13250/21291|13250/21291|4417/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.74G>A|p.Gly25Asp|74/2796|74/2796|25/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2723G>A|||||2723|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4526G>A|||||4526|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*31G>A|||||31|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725299.1|protein_coding||c.*4960G>A|||||4960|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742610.1|protein_coding||c.*4960G>A|||||4960|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3460G>A|||||3460|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3460G>A|||||3460|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2542G>A|||||2542|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2542G>A|||||2542|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1672G>A|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1672G>A|||||1672|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1423G>A|||||1423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*829G>A|||||829|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*829G>A|||||829|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*490G>A|||||490|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*490G>A|||||490|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*73G>A|||||73|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*73G>A|||||73|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*34G>A|||||34|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:729:713,16:713:24566:16:524:0,-173.44,-2080.17
NC_045512.2	13617	.	G	A	12992.0	.	AB=0.366918;ABP=288.526;AC=1;AF=0.5;AN=2;AO=681;CIGAR=1X;DP=1856;DPB=1856;DPRA=0;EPP=4.6971;EPPR=11.4063;GTI=0;LEN=1;MEANALT=3;MQM=50.1747;MQMR=49.3816;NS=1;NUMALT=1;ODDS=2991.51;PAIRED=1;PAIREDR=0.986219;PAO=0;PQA=0;PQR=0;PRO=0;QA=22360;QR=40233;RO=1161;RPL=354;RPP=5.33483;RPPR=1474.54;RPR=327;RUN=1;SAF=324;SAP=6.48274;SAR=357;SRF=609;SRP=9.08706;SRR=552;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13353G>A|p.Lys4451Lys|13353/21291|13353/21291|4451/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.177G>A|p.Lys59Lys|177/2796|177/2796|59/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2620G>A|||||2620|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4423G>A|||||4423|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*134G>A|||||134|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3563G>A|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3563G>A|||||3563|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2645G>A|||||2645|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2645G>A|||||2645|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1775G>A|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1775G>A|||||1775|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1526G>A|||||1526|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1526G>A|||||1526|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*932G>A|||||932|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*932G>A|||||932|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*593G>A|||||593|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*593G>A|||||593|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*176G>A|||||176|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*176G>A|||||176|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*137G>A|||||137|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1856:1161,681:1161:40233:681:22360:-1335.68,0,-2783.93
NC_045512.2	13625	.	ATG	AG	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=43;CIGAR=1M1D1M;DP=1903;DPB=1889;DPRA=0;EPP=3.0608;EPPR=6.04849;GTI=0;LEN=1;MEANALT=2;MQM=45.0698;MQMR=49.6837;NS=1;NUMALT=1;ODDS=2220.17;PAIRED=1;PAIREDR=0.989779;PAO=0.5;PQA=16;PQR=16;PRO=0.5;QA=1368;QR=65600;RO=1859;RPL=0;RPP=96.3836;RPPR=658.308;RPR=43;RUN=1;SAF=22;SAP=3.0608;SAR=21;SRF=946;SRP=4.28235;SRR=913;TYPE=del;ANN=AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13362delT|p.Asp4454fs|13362/21291|13362/21291|4454/7096||,AG|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.186delT|p.Asp62fs|186/2796|186/2796|62/931||WARNING_TRANSCRIPT_NO_START_CODON,AG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2611delT|||||2611|WARNING_TRANSCRIPT_NO_START_CODON,AG|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4414delT|||||4414|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*143delT|||||143|,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3572delT|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3572delT|||||3572|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2654delT|||||2654|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2654delT|||||2654|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1784delT|||||1784|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1784delT|||||1784|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1535delT|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1535delT|||||1535|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*941delT|||||941|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*941delT|||||941|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*602delT|||||602|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*602delT|||||602|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*185delT|||||185|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*185delT|||||185|WARNING_TRANSCRIPT_NO_START_CODON,AG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*146delT|||||146|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1903:1859,43:1859:65600:43:1368:0,-462.878,-5360.42
NC_045512.2	13837	.	C	T	1.77195E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=88;CIGAR=1X;DP=3272;DPB=3272;DPRA=0;EPP=3.0103;EPPR=10.8209;GTI=0;LEN=1;MEANALT=2;MQM=49.4205;MQMR=52.6368;NS=1;NUMALT=1;ODDS=3549.8;PAIRED=1;PAIREDR=0.994031;PAO=0;PQA=0;PQR=0;PRO=0;QA=3060;QR=110447;RO=3183;RPL=37;RPP=7.84676;RPPR=68.1483;RPR=51;RUN=1;SAF=43;SAP=3.109;SAR=45;SRF=1567;SRP=4.64828;SRR=1616;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13573C>T|p.His4525Tyr|13573/21291|13573/21291|4525/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.397C>T|p.His133Tyr|397/2796|397/2796|133/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2400C>T|||||2400|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4203C>T|||||4203|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*354C>T|||||354|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3783C>T|||||3783|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3783C>T|||||3783|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2865C>T|||||2865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2865C>T|||||2865|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*1995C>T|||||1995|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*1995C>T|||||1995|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1746C>T|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1746C>T|||||1746|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1152C>T|||||1152|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1152C>T|||||1152|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*813C>T|||||813|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*813C>T|||||813|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*396C>T|||||396|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*396C>T|||||396|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*357C>T|||||357|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3272:3183,88:3183:110447:88:3060:0,-725.794,-9296.11
NC_045512.2	13884	.	ATA	AA	5.23755E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1M1D1M;DP=3158;DPB=3145.33;DPRA=0;EPP=3.23888;EPPR=12.2236;GTI=0;LEN=1;MEANALT=3;MQM=39.8947;MQMR=52.8608;NS=1;NUMALT=1;ODDS=3980.02;PAIRED=1;PAIREDR=0.994867;PAO=0;PQA=0;PQR=0;PRO=0;QA=1235;QR=110028;RO=3117;RPL=35;RPP=61.5258;RPPR=7.35812;RPR=3;RUN=1;SAF=17;SAP=3.9246;SAR=21;SRF=1529;SRP=5.43535;SRR=1588;TYPE=del;ANN=AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13621delT|p.Tyr4541fs|13621/21291|13621/21291|4541/7096||,AA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.445delT|p.Tyr149fs|445/2796|445/2796|149/931||WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2352delT|||||2352|WARNING_TRANSCRIPT_NO_START_CODON,AA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4155delT|||||4155|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*402delT|||||402|,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3831delT|||||3831|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3831delT|||||3831|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2913delT|||||2913|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2913delT|||||2913|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2043delT|||||2043|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2043delT|||||2043|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1794delT|||||1794|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1794delT|||||1794|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1200delT|||||1200|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1200delT|||||1200|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*861delT|||||861|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*861delT|||||861|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*444delT|||||444|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*444delT|||||444|WARNING_TRANSCRIPT_NO_START_CODON,AA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*405delT|||||405|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3158:3117,38:3117:110028:38:1235:0,-855.492,-9476.37
NC_045512.2	13948	.	G	T	2626.9	.	AB=0.192751;ABP=1925.83;AC=1;AF=0.5;AN=2;AO=452;CIGAR=1X;DP=2345;DPB=2345;DPRA=0;EPP=6.77675;EPPR=40.6702;GTI=0;LEN=1;MEANALT=2;MQM=48.3606;MQMR=50.5876;NS=1;NUMALT=1;ODDS=604.866;PAIRED=1;PAIREDR=0.993118;PAO=0;PQA=0;PQR=0;PRO=0;QA=15755;QR=66219;RO=1889;RPL=442;RPP=899.579;RPPR=13.3849;RPR=10;RUN=1;SAF=212;SAP=6.77675;SAR=240;SRF=915;SRP=7.01183;SRR=974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.13684G>T|p.Asp4562Tyr|13684/21291|13684/21291|4562/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.508G>T|p.Asp170Tyr|508/2796|508/2796|170/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-2289G>T|||||2289|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-4092G>T|||||4092|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*465G>T|||||465|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*3894G>T|||||3894|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*3894G>T|||||3894|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*2976G>T|||||2976|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*2976G>T|||||2976|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2106G>T|||||2106|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2106G>T|||||2106|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*1857G>T|||||1857|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*1857G>T|||||1857|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1263G>T|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1263G>T|||||1263|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*924G>T|||||924|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*924G>T|||||924|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*507G>T|||||507|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*507G>T|||||507|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*468G>T|||||468|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2345:1889,452:1889:66219:452:15755:-591.959,0,-4884.54
NC_045512.2	14343	.	T	C	2.52654E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=243;CIGAR=1X;DP=3163;DPB=3163;DPRA=0;EPP=3.01924;EPPR=13.9019;GTI=0;LEN=1;MEANALT=2;MQM=48.0741;MQMR=53.283;NS=1;NUMALT=1;ODDS=1944.19;PAIRED=0.987654;PAIREDR=0.994176;PAO=0;PQA=0;PQR=0;PRO=0;QA=8382;QR=101644;RO=2919;RPL=136;RPP=10.5256;RPPR=4.51672;RPR=107;RUN=1;SAF=124;SAP=3.2337;SAR=119;SRF=1486;SRP=5.09994;SRR=1433;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14079T>C|p.Cys4693Cys|14079/21291|14079/21291|4693/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.903T>C|p.Cys301Cys|903/2796|903/2796|301/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1894T>C|||||1894|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3697T>C|||||3697|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*860T>C|||||860|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4289T>C|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4289T>C|||||4289|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3371T>C|||||3371|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3371T>C|||||3371|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2501T>C|||||2501|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2501T>C|||||2501|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2252T>C|||||2252|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2252T>C|||||2252|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1658T>C|||||1658|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1658T>C|||||1658|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1319T>C|||||1319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1319T>C|||||1319|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*902T>C|||||902|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*902T>C|||||902|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*863T>C|||||863|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3163:2919,243:2919:101644:243:8382:0,-256.43,-8135.24
NC_045512.2	14408	.	C	T	85570.9	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2863;CIGAR=1X;DP=2866;DPB=2866;DPRA=0;EPP=6.02063;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=51.4149;MQMR=52;NS=1;NUMALT=1;ODDS=3935.49;PAIRED=0.991966;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100761;QR=108;RO=3;RPL=1519;RPP=26.2382;RPPR=3.73412;RPR=1344;RUN=1;SAF=1438;SAP=3.13848;SAR=1425;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14144C>T|p.Pro4715Leu|14144/21291|14144/21291|4715/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.968C>T|p.Pro323Leu|968/2796|968/2796|323/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1829C>T|||||1829|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3632C>T|||||3632|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*925C>T|||||925|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4354C>T|||||4354|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3436C>T|||||3436|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2566C>T|||||2566|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2317C>T|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1723C>T|||||1723|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1384C>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*967C>T|||||967|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*928C>T|||||928|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2866:3,2863:3:108:2863:100761:-8563.93,-852.723,0
NC_045512.2	14599	.	C	T	10548.1	.	AB=0.325339;ABP=511.234;AC=1;AF=0.5;AN=2;AO=624;CIGAR=1X;DP=1918;DPB=1918;DPRA=0;EPP=4.1378;EPPR=15.144;GTI=0;LEN=1;MEANALT=2;MQM=45.7196;MQMR=51.9281;NS=1;NUMALT=1;ODDS=2428.8;PAIRED=0.983974;PAIREDR=0.992266;PAO=0;PQA=0;PQR=0;PRO=0;QA=22070;QR=44878;RO=1293;RPL=147;RPP=381.974;RPPR=21.5258;RPR=477;RUN=1;SAF=324;SAP=5.01474;SAR=300;SRF=649;SRP=3.05229;SRR=644;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14335C>T|p.Leu4779Leu|14335/21291|14335/21291|4779/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1159C>T|p.Leu387Leu|1159/2796|1159/2796|387/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1638C>T|||||1638|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3441C>T|||||3441|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1116C>T|||||1116|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4545C>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4545C>T|||||4545|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3627C>T|||||3627|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3627C>T|||||3627|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2757C>T|||||2757|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2757C>T|||||2757|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2508C>T|||||2508|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2508C>T|||||2508|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1914C>T|||||1914|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1914C>T|||||1914|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1575C>T|||||1575|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1575C>T|||||1575|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1158C>T|||||1158|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1158C>T|||||1158|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1119C>T|||||1119|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1918:1293,624:1293:44878:624:22070:-1154.93,0,-3270.18
NC_045512.2	14676	.	C	T	4.51306E-13	.	AB=0.129404;ABP=3423.16;AC=1;AF=0.5;AN=2;AO=371;CIGAR=1X;DP=2867;DPB=2867;DPRA=0;EPP=3.06298;EPPR=4.0168;GTI=0;LEN=1;MEANALT=3;MQM=50.1213;MQMR=52.666;NS=1;NUMALT=1;ODDS=370.612;PAIRED=0.994609;PAIREDR=0.989575;PAO=0;PQA=0;PQR=0;PRO=0;QA=13140;QR=85679;RO=2494;RPL=194;RPP=4.70182;RPPR=46.6975;RPR=177;RUN=1;SAF=190;SAP=3.4844;SAR=181;SRF=1273;SRP=5.36461;SRR=1221;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14412C>T|p.Pro4804Pro|14412/21291|14412/21291|4804/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1236C>T|p.Pro412Pro|1236/2796|1236/2796|412/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1561C>T|||||1561|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3364C>T|||||3364|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4945C>T|||||4945|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1193C>T|||||1193|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4622C>T|||||4622|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4622C>T|||||4622|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3704C>T|||||3704|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3704C>T|||||3704|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2585C>T|||||2585|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2585C>T|||||2585|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*1991C>T|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*1991C>T|||||1991|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1652C>T|||||1652|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1652C>T|||||1652|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1235C>T|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1235C>T|||||1235|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1196C>T|||||1196|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2867:2494,371:2494:85679:371:13140:-229.956,0,-6526.74
NC_045512.2	14925	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1720;DPB=1720;DPRA=0;EPP=3.52123;EPPR=14.8804;GTI=0;LEN=1;MEANALT=2;MQM=52.1912;MQMR=50.3628;NS=1;NUMALT=1;ODDS=1662.43;PAIRED=1;PAIREDR=0.992126;PAO=0;PQA=0;PQR=0;PRO=0;QA=2343;QR=57307;RO=1651;RPL=10;RPP=76.5849;RPPR=99.6033;RPR=58;RUN=1;SAF=36;SAP=3.52123;SAR=32;SRF=819;SRP=3.23258;SRR=832;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14661C>T|p.Val4887Val|14661/21291|14661/21291|4887/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1485C>T|p.Val495Val|1485/2796|1485/2796|495/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1312C>T|||||1312|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3115C>T|||||3115|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4696C>T|||||4696|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1442C>T|||||1442|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4871C>T|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4871C>T|||||4871|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3953C>T|||||3953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3953C>T|||||3953|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3083C>T|||||3083|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3083C>T|||||3083|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2834C>T|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2240C>T|||||2240|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2240C>T|||||2240|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1901C>T|||||1901|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1901C>T|||||1901|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1484C>T|||||1484|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1484C>T|||||1484|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1445C>T|||||1445|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1720:1651,68:1651:57307:68:2343:0,-314.394,-4648.27
NC_045512.2	14960	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=1845;DPB=1845;DPRA=0;EPP=3.0103;EPPR=4.84214;GTI=0;LEN=1;MEANALT=1;MQM=49.7381;MQMR=51.802;NS=1;NUMALT=1;ODDS=2084.32;PAIRED=1;PAIREDR=0.988353;PAO=0;PQA=0;PQR=0;PRO=0;QA=1500;QR=63751;RO=1803;RPL=16;RPP=8.18047;RPPR=133.372;RPR=26;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=915;SRP=3.88828;SRR=888;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14696A>T|p.Asn4899Ile|14696/21291|14696/21291|4899/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1520A>T|p.Asn507Ile|1520/2796|1520/2796|507/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1277A>T|||||1277|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-3080A>T|||||3080|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4661A>T|||||4661|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1477A>T|||||1477|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725300.1|protein_coding||c.*4906A>T|||||4906|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742611.1|protein_coding||c.*4906A>T|||||4906|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*3988A>T|||||3988|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*3988A>T|||||3988|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3118A>T|||||3118|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3118A>T|||||3118|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2869A>T|||||2869|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2869A>T|||||2869|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2275A>T|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2275A>T|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*1936A>T|||||1936|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*1936A>T|||||1936|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1519A>T|||||1519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1519A>T|||||1519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1480A>T|||||1480|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1845:1803,42:1803:63751:42:1500:0,-430.383,-5341.54
NC_045512.2	15081	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=19;CIGAR=1X;DP=1823;DPB=1823;DPRA=0;EPP=3.12459;EPPR=3.49285;GTI=0;LEN=1;MEANALT=3;MQM=48.7368;MQMR=52.8733;NS=1;NUMALT=1;ODDS=2311.42;PAIRED=1;PAIREDR=0.986667;PAO=0;PQA=0;PQR=0;PRO=0;QA=628;QR=61997;RO=1800;RPL=12;RPP=5.8675;RPPR=27.3356;RPR=7;RUN=1;SAF=10;SAP=3.12459;SAR=9;SRF=897;SRP=3.05373;SRR=903;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14817C>A|p.Ala4939Ala|14817/21291|14817/21291|4939/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1641C>A|p.Ala547Ala|1641/2796|1641/2796|547/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1156C>A|||||1156|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2959C>A|||||2959|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4540C>A|||||4540|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1598C>A|||||1598|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4109C>A|||||4109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4109C>A|||||4109|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3239C>A|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3239C>A|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*2990C>A|||||2990|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*2990C>A|||||2990|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2396C>A|||||2396|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2396C>A|||||2396|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2057C>A|||||2057|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2057C>A|||||2057|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1640C>A|||||1640|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1640C>A|||||1640|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1601C>A|||||1601|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1823:1800,19:1800:61997:19:628:0,-496.547,-5321.06
NC_045512.2	15099	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1724;DPB=1724;DPRA=0;EPP=3.0103;EPPR=3.87276;GTI=0;LEN=1;MEANALT=2;MQM=54.1;MQMR=53.9871;NS=1;NUMALT=1;ODDS=2154.41;PAIRED=1;PAIREDR=0.9953;PAO=0;PQA=0;PQR=0;PRO=0;QA=661;QR=57848;RO=1702;RPL=8;RPP=4.74748;RPPR=3.03071;RPR=12;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=831;SRP=5.05164;SRR=871;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14835A>G|p.Arg4945Arg|14835/21291|14835/21291|4945/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1659A>G|p.Arg553Arg|1659/2796|1659/2796|553/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1138A>G|||||1138|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2941A>G|||||2941|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4522A>G|||||4522|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1616A>G|||||1616|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4127A>G|||||4127|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4127A>G|||||4127|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3257A>G|||||3257|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3257A>G|||||3257|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3008A>G|||||3008|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3008A>G|||||3008|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2414A>G|||||2414|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2414A>G|||||2414|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2075A>G|||||2075|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2075A>G|||||2075|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1658A>G|||||1658|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1658A>G|||||1658|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1619A>G|||||1619|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1724:1702,20:1702:57848:20:661:0,-459.131,-5019.76
NC_045512.2	15112	.	G	A	2.45301E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1742;DPB=1742;DPRA=0;EPP=3.0103;EPPR=7.71074;GTI=0;LEN=1;MEANALT=2;MQM=51.5;MQMR=53.8941;NS=1;NUMALT=1;ODDS=2148.09;PAIRED=1;PAIREDR=0.993601;PAO=0;PQA=0;PQR=0;PRO=0;QA=784;QR=59941;RO=1719;RPL=12;RPP=3.40511;RPPR=4.73965;RPR=10;RUN=1;SAF=11;SAP=3.0103;SAR=11;SRF=842;SRP=4.55774;SRR=877;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.14848G>A|p.Ala4950Thr|14848/21291|14848/21291|4950/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1672G>A|p.Ala558Thr|1672/2796|1672/2796|558/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-1125G>A|||||1125|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2928G>A|||||2928|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4509G>A|||||4509|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1629G>A|||||1629|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4140G>A|||||4140|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4140G>A|||||4140|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3270G>A|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3270G>A|||||3270|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3021G>A|||||3021|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3021G>A|||||3021|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2088G>A|||||2088|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2088G>A|||||2088|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1671G>A|||||1671|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1671G>A|||||1671|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1632G>A|||||1632|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1742:1719,22:1719:59941:22:784:0,-454.638,-5189.54
NC_045512.2	15279	.	C	T	15999.3	.	AB=0.501107;ABP=3.02472;AC=1;AF=0.5;AN=2;AO=679;CIGAR=1X;DP=1355;DPB=1355;DPRA=0;EPP=3.72986;EPPR=5.54368;GTI=0;LEN=1;MEANALT=3;MQM=50.6848;MQMR=52.4911;NS=1;NUMALT=1;ODDS=3683.98;PAIRED=0.997054;PAIREDR=0.997024;PAO=0;PQA=0;PQR=0;PRO=0;QA=23811;QR=23325;RO=672;RPL=353;RPP=5.34167;RPPR=13.1438;RPR=326;RUN=1;SAF=347;SAP=3.72986;SAR=332;SRF=340;SRP=3.21711;SRR=332;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15015C>T|p.His5005His|15015/21291|15015/21291|5005/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.1839C>T|p.His613His|1839/2796|1839/2796|613/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-958C>T|||||958|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2761C>T|||||2761|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4342C>T|||||4342|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1796C>T|||||1796|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4307C>T|||||4307|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4307C>T|||||4307|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3437C>T|||||3437|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3437C>T|||||3437|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3188C>T|||||3188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3188C>T|||||3188|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2594C>T|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2594C>T|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2255C>T|||||2255|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2255C>T|||||2255|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*1838C>T|||||1838|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*1838C>T|||||1838|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1799C>T|||||1799|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1355:672,679:672:23325:679:23811:-1608.52,0,-1621.57
NC_045512.2	15451	.	G	A	8929.57	.	AB=0.4;ABP=95.515;AC=1;AF=0.5;AN=2;AO=426;CIGAR=1X;DP=1065;DPB=1065;DPRA=0;EPP=3.52004;EPPR=4.50892;GTI=0;LEN=1;MEANALT=1;MQM=48.9977;MQMR=53.4648;NS=1;NUMALT=1;ODDS=2056.11;PAIRED=0.985915;PAIREDR=0.984351;PAO=0;PQA=0;PQR=0;PRO=0;QA=15055;QR=22076;RO=639;RPL=213;RPP=3.0103;RPPR=25.3061;RPR=213;RUN=1;SAF=209;SAP=3.33653;SAR=217;SRF=315;SRP=3.28556;SRR=324;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15187G>A|p.Gly5063Ser|15187/21291|15187/21291|5063/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2011G>A|p.Gly671Ser|2011/2796|2011/2796|671/931||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-786G>A|||||786|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2589G>A|||||2589|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4170G>A|||||4170|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*1968G>A|||||1968|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4479G>A|||||4479|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4479G>A|||||4479|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3609G>A|||||3609|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3609G>A|||||3609|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3360G>A|||||3360|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3360G>A|||||3360|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2766G>A|||||2766|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2766G>A|||||2766|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2427G>A|||||2427|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2010G>A|||||2010|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2010G>A|||||2010|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*1971G>A|||||1971|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1065:639,426:639:22076:426:15055:-910.196,0,-1597.03
NC_045512.2	15610	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1X;DP=2649;DPB=2649;DPRA=0;EPP=3.0459;EPPR=3.03128;GTI=0;LEN=1;MEANALT=2;MQM=49.2623;MQMR=53.041;NS=1;NUMALT=1;ODDS=2973.3;PAIRED=1;PAIREDR=0.993815;PAO=0;PQA=0;PQR=0;PRO=0;QA=2160;QR=90654;RO=2587;RPL=26;RPP=5.89373;RPPR=286.352;RPR=35;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1324;SRP=6.13363;SRR=1263;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15346C>T|p.Gln5116*|15346/21291|15346/21291|5116/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2170C>T|p.Gln724*|2170/2796|2170/2796|724/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-627C>T|||||627|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2430C>T|||||2430|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-4011C>T|||||4011|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2127C>T|||||2127|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4638C>T|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4638C>T|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3768C>T|||||3768|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3768C>T|||||3768|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3519C>T|||||3519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3519C>T|||||3519|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2925C>T|||||2925|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2925C>T|||||2925|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2586C>T|||||2586|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2586C>T|||||2586|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2169C>T|||||2169|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2169C>T|||||2169|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2130C>T|||||2130|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2649:2587,61:2587:90654:61:2160:0,-613.681,-7700.41
NC_045512.2	15682	.	TATT	AATA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X2M1X;DP=3135;DPB=3136;DPRA=0;EPP=3.15039;EPPR=3.32274;GTI=0;LEN=4;MEANALT=6;MQM=44.4677;MQMR=52.7775;NS=1;NUMALT=1;ODDS=3669.8;PAIRED=0.903226;PAIREDR=0.995432;PAO=3;PQA=100;PQR=0;PRO=1;QA=2133;QR=107768;RO=3065;RPL=25;RPP=8.05372;RPPR=14.0802;RPR=37;RUN=1;SAF=31;SAP=3.0103;SAR=31;SRF=1555;SRP=4.44496;SRR=1510;TYPE=complex;ANN=AATA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15418_15421delTATTinsAATA|p.TyrLeu5140AsnMet|15418/21291|15418/21291|5140/7096||,AATA|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2242_2245delTATTinsAATA|p.TyrLeu748AsnMet|2242/2796|2242/2796|748/931||WARNING_TRANSCRIPT_NO_START_CODON,AATA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-555_-552delTATTinsAATA|||||555|WARNING_TRANSCRIPT_NO_START_CODON,AATA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2358_-2355delTATTinsAATA|||||2358|WARNING_TRANSCRIPT_NO_START_CODON,AATA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3939_-3936delTATTinsAATA|||||3939|WARNING_TRANSCRIPT_NO_START_CODON,AATA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4977_-4974delTATTinsAATA|||||4977|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2199_*2202delTATTinsAATA|||||2199|,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4710_*4713delTATTinsAATA|||||4710|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4710_*4713delTATTinsAATA|||||4710|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3840_*3843delTATTinsAATA|||||3840|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3840_*3843delTATTinsAATA|||||3840|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3591_*3594delTATTinsAATA|||||3591|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3591_*3594delTATTinsAATA|||||3591|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*2997_*3000delTATTinsAATA|||||2997|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*2997_*3000delTATTinsAATA|||||2997|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2658_*2661delTATTinsAATA|||||2658|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2658_*2661delTATTinsAATA|||||2658|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2241_*2244delTATTinsAATA|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2241_*2244delTATTinsAATA|||||2241|WARNING_TRANSCRIPT_NO_START_CODON,AATA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2202_*2205delTATTinsAATA|||||2202|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3135:3065,62:3065:107768:62:2133:0,-777.887,-9178.74
NC_045512.2	15765	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2620;DPB=2620;DPRA=0;EPP=3.08518;EPPR=7.23508;GTI=0;LEN=1;MEANALT=1;MQM=53.8621;MQMR=53.0471;NS=1;NUMALT=1;ODDS=3289.28;PAIRED=1;PAIREDR=0.990351;PAO=0;PQA=0;PQR=0;PRO=0;QA=963;QR=91316;RO=2591;RPL=13;RPP=3.68421;RPPR=13.7118;RPR=16;RUN=1;SAF=14;SAP=3.08518;SAR=15;SRF=1248;SRP=10.574;SRR=1343;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15501A>G|p.Leu5167Leu|15501/21291|15501/21291|5167/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2325A>G|p.Leu775Leu|2325/2796|2325/2796|775/931||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-472A>G|||||472|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2275A>G|||||2275|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3856A>G|||||3856|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4894A>G|||||4894|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2282A>G|||||2282|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4793A>G|||||4793|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4793A>G|||||4793|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*3923A>G|||||3923|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*3923A>G|||||3923|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3674A>G|||||3674|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3674A>G|||||3674|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3080A>G|||||3080|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3080A>G|||||3080|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2741A>G|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2741A>G|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2324A>G|||||2324|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2324A>G|||||2324|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2285A>G|||||2285|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2620:2591,29:2591:91316:29:963:0,-703.357,-7841.25
NC_045512.2	15924	.	C	T	6.44918E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=3061;DPB=3061;DPRA=0;EPP=3.06899;EPPR=5.95155;GTI=0;LEN=1;MEANALT=1;MQM=41.2703;MQMR=52.1574;NS=1;NUMALT=1;ODDS=3840.84;PAIRED=0.972973;PAIREDR=0.98578;PAO=0;PQA=0;PQR=0;PRO=0;QA=1310;QR=105103;RO=3024;RPL=10;RPP=19.9713;RPPR=26.2761;RPR=27;RUN=1;SAF=18;SAP=3.06899;SAR=19;SRF=1538;SRP=4.95199;SRR=1486;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15660C>T|p.Tyr5220Tyr|15660/21291|15660/21291|5220/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2484C>T|p.Tyr828Tyr|2484/2796|2484/2796|828/931||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-313C>T|||||313|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-2116C>T|||||2116|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3697C>T|||||3697|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4735C>T|||||4735|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2441C>T|||||2441|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725301.1|protein_coding||c.*4952C>T|||||4952|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742612.1|protein_coding||c.*4952C>T|||||4952|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4082C>T|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4082C>T|||||4082|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3833C>T|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3833C>T|||||3833|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3239C>T|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3239C>T|||||3239|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*2900C>T|||||2900|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*2900C>T|||||2900|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2483C>T|||||2483|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2483C>T|||||2483|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2444C>T|||||2444|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3061:3024,37:3024:105103:37:1310:0,-825.97,-8954.61
NC_045512.2	16047	.	T	C	7.54104E-13	.	AB=0.115049;ABP=4578.78;AC=1;AF=0.5;AN=2;AO=409;CIGAR=1X;DP=3555;DPB=3555;DPRA=0;EPP=3.27045;EPPR=3.01306;GTI=0;LEN=1;MEANALT=2;MQM=49.6186;MQMR=53.0083;NS=1;NUMALT=1;ODDS=928.295;PAIRED=0.99511;PAIREDR=0.992048;PAO=0;PQA=0;PQR=0;PRO=0;QA=14401;QR=109684;RO=3144;RPL=183;RPP=12.8271;RPPR=10.4806;RPR=226;RUN=1;SAF=206;SAP=3.05808;SAR=203;SRF=1597;SRP=4.73698;SRR=1547;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15783T>C|p.Leu5261Leu|15783/21291|15783/21291|5261/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2607T>C|p.Leu869Leu|2607/2796|2607/2796|869/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-190T>C|||||190|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1993T>C|||||1993|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3574T>C|||||3574|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4612T>C|||||4612|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2564T>C|||||2564|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4205T>C|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4205T>C|||||4205|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*3956T>C|||||3956|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*3956T>C|||||3956|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3362T>C|||||3362|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3362T>C|||||3362|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3023T>C|||||3023|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3023T>C|||||3023|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2606T>C|||||2606|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2606T>C|||||2606|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2567T>C|||||2567|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3555:3144,409:3144:109684:409:14401:-124.324,0,-8453.5
NC_045512.2	16176	.	T	C	0.0	.	AB=0.113668;ABP=2820.07;AC=1;AF=0.5;AN=2;AO=247;CIGAR=1X;DP=2173;DPB=2173;DPRA=0;EPP=4.49604;EPPR=9.35551;GTI=0;LEN=1;MEANALT=2;MQM=45.5789;MQMR=50.2919;NS=1;NUMALT=1;ODDS=754.39;PAIRED=0.991903;PAIREDR=0.987532;PAO=0;PQA=0;PQR=0;PRO=0;QA=8569;QR=68076;RO=1925;RPL=193;RPP=172.869;RPPR=930.989;RPR=54;RUN=1;SAF=119;SAP=3.7224;SAR=128;SRF=944;SRP=4.55458;SRR=981;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.15912T>C|p.Thr5304Thr|15912/21291|15912/21291|5304/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding|2/2|c.2736T>C|p.Thr912Thr|2736/2796|2736/2796|912/931||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.-61T>C|||||61|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1864T>C|||||1864|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3445T>C|||||3445|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4483T>C|||||4483|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2693T>C|||||2693|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4334T>C|||||4334|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4334T>C|||||4334|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4085T>C|||||4085|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4085T>C|||||4085|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3491T>C|||||3491|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3491T>C|||||3491|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3152T>C|||||3152|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3152T>C|||||3152|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*2735T>C|||||2735|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*2735T>C|||||2735|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2696T>C|||||2696|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2173:1925,247:1925:68076:247:8569:-17.686,0,-5092.92
NC_045512.2	16466	.	C	T	43588.1	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1613;CIGAR=1X;DP=1646;DPB=1646;DPRA=0;EPP=5.98413;EPPR=3.0761;GTI=0;LEN=1;MEANALT=1;MQM=46.0539;MQMR=52.5455;NS=1;NUMALT=1;ODDS=1904.12;PAIRED=0.989461;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=56743;QR=1140;RO=33;RPL=677;RPP=93.3169;RPPR=22.0271;RPR=936;RUN=1;SAF=821;SAP=4.14248;SAR=792;SRF=16;SRP=3.0761;SRR=17;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16202C>T|p.Pro5401Leu|16202/21291|16202/21291|5401/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.230C>T|p.Pro77Leu|230/1803|230/1803|77/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1574C>T|||||1574|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-3155C>T|||||3155|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-4193C>T|||||4193|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*2983C>T|||||2983|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4624C>T|||||4624|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4624C>T|||||4624|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4375C>T|||||4375|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4375C>T|||||4375|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*3781C>T|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*3781C>T|||||3781|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3442C>T|||||3442|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3442C>T|||||3442|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3025C>T|||||3025|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3025C>T|||||3025|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*2986C>T|||||2986|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*230C>T|||||230|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:1646:33,1613:33:1140:1613:56743:-4368.86,-393.99,0
NC_045512.2	16816	.	C	T	4316.69	.	AB=0.255301;ABP=616.196;AC=1;AF=0.5;AN=2;AO=301;CIGAR=1X;DP=1179;DPB=1179;DPRA=0;EPP=3.19065;EPPR=6.96743;GTI=0;LEN=1;MEANALT=1;MQM=47.6346;MQMR=51.0182;NS=1;NUMALT=1;ODDS=993.955;PAIRED=1;PAIREDR=0.989749;PAO=0;PQA=0;PQR=0;PRO=0;QA=10614;QR=30734;RO=878;RPL=107;RPP=57.6145;RPPR=418.756;RPR=194;RUN=1;SAF=154;SAP=3.3638;SAR=147;SRF=427;SRP=4.43486;SRR=451;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16552C>T|p.Gln5518*|16552/21291|16552/21291|5518/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.580C>T|p.Gln194*|580/1803|580/1803|194/600||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4747C>T|||||4747|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-1224C>T|||||1224|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2805C>T|||||2805|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3843C>T|||||3843|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3333C>T|||||3333|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725302.1|protein_coding||c.*4974C>T|||||4974|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742613.1|protein_coding||c.*4974C>T|||||4974|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725303.1|protein_coding||c.*4725C>T|||||4725|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742614.1|protein_coding||c.*4725C>T|||||4725|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4131C>T|||||4131|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4131C>T|||||4131|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*3792C>T|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*3792C>T|||||3792|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3375C>T|||||3375|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3375C>T|||||3375|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3336C>T|||||3336|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*580C>T|||||580|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1179:878,301:878:30734:301:10614:-508.866,0,-2253.86
NC_045512.2	17218	.	G	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2615;DPB=2615;DPRA=0;EPP=3.07234;EPPR=4.04173;GTI=0;LEN=1;MEANALT=2;MQM=53.2286;MQMR=53.1377;NS=1;NUMALT=1;ODDS=3202.13;PAIRED=1;PAIREDR=0.993796;PAO=0;PQA=0;PQR=0;PRO=0;QA=1252;QR=91012;RO=2579;RPL=12;RPP=10.5174;RPPR=149.422;RPR=23;RUN=1;SAF=18;SAP=3.07234;SAR=17;SRF=1302;SRP=3.53654;SRR=1277;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.16954G>C|p.Asp5652His|16954/21291|16954/21291|5652/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.982G>C|p.Asp328His|982/1803|982/1803|328/600||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-4345G>C|||||4345|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-822G>C|||||822|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-2403G>C|||||2403|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-3441G>C|||||3441|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*3735G>C|||||3735|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725304.1|protein_coding||c.*4533G>C|||||4533|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742615.1|protein_coding||c.*4533G>C|||||4533|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4194G>C|||||4194|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4194G>C|||||4194|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*3777G>C|||||3777|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*3777G>C|||||3777|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*3738G>C|||||3738|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*982G>C|||||982|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2615:2579,35:2579:91012:35:1252:0,-677.895,-7808.81
NC_045512.2	17814	.	G	A	1651.02	.	AB=0.17202;ABP=1312.03;AC=1;AF=0.5;AN=2;AO=241;CIGAR=1X;DP=1401;DPB=1401;DPRA=0;EPP=3.09139;EPPR=3.13031;GTI=0;LEN=1;MEANALT=2;MQM=51.8548;MQMR=52.8454;NS=1;NUMALT=1;ODDS=380.16;PAIRED=0.983402;PAIREDR=0.992228;PAO=0;PQA=0;PQR=0;PRO=0;QA=8561;QR=40234;RO=1158;RPL=118;RPP=3.23556;RPPR=37.6939;RPR=123;RUN=1;SAF=120;SAP=3.01931;SAR=121;SRF=590;SRP=3.91789;SRR=568;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.17550G>A|p.Leu5850Leu|17550/21291|17550/21291|5850/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding|1/1|c.1578G>A|p.Leu526Leu|1578/1803|1578/1803|526/600||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-3749G>A|||||3749|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.-226G>A|||||226|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1807G>A|||||1807|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2845G>A|||||2845|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01.2|protein_coding||c.*4331G>A|||||4331|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725305.1|protein_coding||c.*4790G>A|||||4790|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742616.1|protein_coding||c.*4790G>A|||||4790|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725306.1|protein_coding||c.*4373G>A|||||4373|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009742617.1|protein_coding||c.*4373G>A|||||4373|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725312.1|protein_coding||c.*4334G>A|||||4334|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*1578G>A|||||1578|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1401:1158,241:1158:40234:241:8561:-314.533,0,-3073.09
NC_045512.2	18564	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2012;DPB=2012;DPRA=0;EPP=3.0103;EPPR=4.27426;GTI=0;LEN=1;MEANALT=1;MQM=38.3077;MQMR=52.5287;NS=1;NUMALT=1;ODDS=2535.91;PAIRED=1;PAIREDR=0.984894;PAO=0;PQA=0;PQR=0;PRO=0;QA=919;QR=69984;RO=1986;RPL=0;RPP=59.4686;RPPR=40.0281;RPR=26;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=971;SRP=5.1271;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18300A>C|p.Lys6100Asn|18300/21291|18300/21291|6100/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.525A>C|p.Lys175Asn|525/1581|525/1581|175/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2999A>C|||||2999|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1057A>C|||||1057|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2095A>C|||||2095|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2328A>C|||||2328|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*525A>C|||||525|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2012:1986,26:1986:69984:26:919:0,-543.43,-5961.14
NC_045512.2	18585	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=34;CIGAR=1X;DP=1713;DPB=1713;DPRA=0;EPP=12.2071;EPPR=3.19799;GTI=0;LEN=1;MEANALT=3;MQM=54.7647;MQMR=52.0816;NS=1;NUMALT=1;ODDS=2102.51;PAIRED=1;PAIREDR=0.991597;PAO=0;PQA=0;PQR=0;PRO=0;QA=599;QR=49685;RO=1666;RPL=24;RPP=15.5282;RPPR=146.677;RPR=10;RUN=1;SAF=33;SAP=68.4099;SAR=1;SRF=784;SRP=15.5282;SRR=882;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18321A>G|p.Val6107Val|18321/21291|18321/21291|6107/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.546A>G|p.Val182Val|546/1581|546/1581|182/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2978A>G|||||2978|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1036A>G|||||1036|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2074A>G|||||2074|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2349A>G|||||2349|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*546A>G|||||546|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1713:1666,34:1666:49685:34:599:0,-457.977,-4212.18
NC_045512.2	18589	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=1666;DPB=1666;DPRA=0;EPP=28.0461;EPPR=3.12058;GTI=0;LEN=1;MEANALT=3;MQM=54.6029;MQMR=51.9078;NS=1;NUMALT=1;ODDS=1835.86;PAIRED=1;PAIREDR=0.992476;PAO=0;PQA=0;PQR=0;PRO=0;QA=1260;QR=50241;RO=1595;RPL=48;RPP=28.0461;RPPR=206.91;RPR=20;RUN=1;SAF=68;SAP=150.67;SAR=0;SRF=729;SRP=28.5629;SRR=866;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18325G>T|p.Val6109Phe|18325/21291|18325/21291|6109/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.550G>T|p.Val184Phe|550/1581|550/1581|184/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2974G>T|||||2974|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1032G>T|||||1032|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2070G>T|||||2070|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2353G>T|||||2353|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*550G>T|||||550|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1666:1595,68:1595:50241:68:1260:0,-389.132,-4187.65
NC_045512.2	18591	.	C	A,G	0.0	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=22,53;CIGAR=1X,1X;DP=1626;DPB=1626;DPRA=0,0;EPP=17.2236,21.0786;EPPR=5.84906;GTI=0;LEN=1,1;MEANALT=3,3;MQM=52.2273,56;MQMR=51.7076;NS=1;NUMALT=2;ODDS=1862.57;PAIRED=0.909091,1;PAIREDR=0.993544;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=349,899;QR=45627;RO=1549;RPL=16,37;RPP=12.8806,21.0786;RPPR=195.963;RPR=6,16;RUN=1,1;SAF=21,53;SAP=42.4916,118.098;SAR=1,0;SRF=701;SRP=33.303;SRR=848;TYPE=snp,snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18327C>A|p.Val6109Val|18327/21291|18327/21291|6109/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18327C>G|p.Val6109Val|18327/21291|18327/21291|6109/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.552C>A|p.Val184Val|552/1581|552/1581|184/526||WARNING_TRANSCRIPT_NO_START_CODON,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.552C>G|p.Val184Val|552/1581|552/1581|184/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2972C>A|||||2972|,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2972C>G|||||2972|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1030C>A|||||1030|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1030C>G|||||1030|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2068C>A|||||2068|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2068C>G|||||2068|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2355C>A|||||2355|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2355C>G|||||2355|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*552C>A|||||552|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*552C>G|||||552|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1626:1549,22,53:1549:45627:22,53:349,899:0,-442.675,-3865.33,-402.972,-3808.63,-3816.3
NC_045512.2	18596	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1560;DPB=1560;DPRA=0;EPP=37.7539;EPPR=7.02588;GTI=0;LEN=1;MEANALT=3;MQM=54.8611;MQMR=51.6866;NS=1;NUMALT=1;ODDS=1910.29;PAIRED=1;PAIREDR=0.994733;PAO=0;PQA=0;PQR=0;PRO=0;QA=597;QR=47340;RO=1519;RPL=30;RPP=37.7539;RPPR=206.189;RPR=6;RUN=1;SAF=34;SAP=64.7766;SAR=2;SRF=706;SRP=19.3771;SRR=813;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18332G>T|p.Trp6111Leu|18332/21291|18332/21291|6111/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.557G>T|p.Trp186Leu|557/1581|557/1581|186/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2967G>T|||||2967|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1025G>T|||||1025|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2063G>T|||||2063|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2360G>T|||||2360|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*557G>T|||||557|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1560:1519,36:1519:47340:36:597:0,-415.548,-3982.11
NC_045512.2	18607	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=37;CIGAR=1X;DP=2032;DPB=2032;DPRA=0;EPP=45.7942;EPPR=35.685;GTI=0;LEN=1;MEANALT=2;MQM=52.7297;MQMR=50.0191;NS=1;NUMALT=1;ODDS=2562.27;PAIRED=1;PAIREDR=0.993967;PAO=0;PQA=0;PQR=0;PRO=0;QA=596;QR=62548;RO=1989;RPL=33;RPP=52.3673;RPPR=39.5716;RPR=4;RUN=1;SAF=36;SAP=74.9036;SAR=1;SRF=984;SRP=3.49176;SRR=1005;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18343T>G|p.Phe6115Val|18343/21291|18343/21291|6115/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.568T>G|p.Phe190Val|568/1581|568/1581|190/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2956T>G|||||2956|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-1014T>G|||||1014|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2052T>G|||||2052|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2371T>G|||||2371|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*568T>G|||||568|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2032:1989,37:1989:62548:37:596:0,-558.569,-5124.76
NC_045512.2	18634	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=30;CIGAR=1X;DP=2484;DPB=2484;DPRA=0;EPP=68.1545;EPPR=20.1139;GTI=0;LEN=1;MEANALT=2;MQM=55.0333;MQMR=49.1239;NS=1;NUMALT=1;ODDS=3237.29;PAIRED=1;PAIREDR=0.991031;PAO=0;PQA=0;PQR=0;PRO=0;QA=541;QR=83732;RO=2453;RPL=30;RPP=68.1545;RPPR=122.241;RPR=0;RUN=1;SAF=30;SAP=68.1545;SAR=0;SRF=1223;SRP=3.05368;SRR=1230;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18370G>T|p.Val6124Leu|18370/21291|18370/21291|6124/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.595G>T|p.Val199Leu|595/1581|595/1581|199/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2929G>T|||||2929|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-987G>T|||||987|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-2025G>T|||||2025|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2398G>T|||||2398|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*595G>T|||||595|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2484:2453,30:2453:83732:30:541:0,-698.736,-6808.01
NC_045512.2	18977	.	A	G	0.0	.	AB=0.128648;ABP=4723.57;AC=1;AF=0.5;AN=2;AO=507;CIGAR=1X;DP=3941;DPB=3941;DPRA=0;EPP=3.97397;EPPR=3.34491;GTI=0;LEN=1;MEANALT=2;MQM=47.2308;MQMR=50.4512;NS=1;NUMALT=1;ODDS=685.817;PAIRED=1;PAIREDR=0.993009;PAO=0;PQA=0;PQR=0;PRO=0;QA=17828;QR=120870;RO=3433;RPL=192;RPP=67.8076;RPPR=178.682;RPR=315;RUN=1;SAF=262;SAP=4.24808;SAR=245;SRF=1718;SRP=3.01599;SRR=1715;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18713A>G|p.Gln6238Arg|18713/21291|18713/21291|6238/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.938A>G|p.Gln313Arg|938/1581|938/1581|313/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2586A>G|||||2586|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-644A>G|||||644|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1682A>G|||||1682|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2741A>G|||||2741|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*938A>G|||||938|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3941:3433,507:3433:120870:507:17828:-246.189,0,-8997.03
NC_045512.2	19132	.	G	T	1.25365E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=135;CIGAR=1X;DP=5691;DPB=5691;DPRA=0;EPP=3.02638;EPPR=3.2745;GTI=0;LEN=1;MEANALT=1;MQM=46.3778;MQMR=52.194;NS=1;NUMALT=1;ODDS=6443.64;PAIRED=0.97037;PAIREDR=0.991901;PAO=0;PQA=0;PQR=0;PRO=0;QA=4554;QR=195166;RO=5556;RPL=89;RPP=32.7514;RPPR=54.7942;RPR=46;RUN=1;SAF=64;SAP=3.79846;SAR=71;SRF=2759;SRP=3.57466;SRR=2797;TYPE=snp;ANN=T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18868G>T|p.Glu6290*|18868/21291|18868/21291|6290/7096||,T|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1093G>T|p.Glu365*|1093/1581|1093/1581|365/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2431G>T|||||2431|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-489G>T|||||489|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1527G>T|||||1527|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2896G>T|||||2896|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1093G>T|||||1093|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5691:5556,135:5556:195166:135:4554:0,-1352.52,-16428.1
NC_045512.2	19137	.	A	C	2.02509E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=114;CIGAR=1X;DP=5642;DPB=5642;DPRA=0;EPP=3.08649;EPPR=3.18362;GTI=0;LEN=1;MEANALT=3;MQM=44.7807;MQMR=52.2286;NS=1;NUMALT=1;ODDS=6562.91;PAIRED=0.964912;PAIREDR=0.991855;PAO=0;PQA=0;PQR=0;PRO=0;QA=3986;QR=194895;RO=5525;RPL=72;RPP=20.1535;RPPR=6.40959;RPR=42;RUN=1;SAF=56;SAP=3.08649;SAR=58;SRF=2750;SRP=3.25594;SRR=2775;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18873A>C|p.Leu6291Phe|18873/21291|18873/21291|6291/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1098A>C|p.Leu366Phe|1098/1581|1098/1581|366/526||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2426A>C|||||2426|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-484A>C|||||484|WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1522A>C|||||1522|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2901A>C|||||2901|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1098A>C|||||1098|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5642:5525,114:5525:194895:114:3986:0,-1386.34,-16434.9
NC_045512.2	19165	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=172;CIGAR=1X;DP=5857;DPB=5857;DPRA=0;EPP=3.81829;EPPR=8.06357;GTI=0;LEN=1;MEANALT=2;MQM=50.7733;MQMR=52.3231;NS=1;NUMALT=1;ODDS=6177.91;PAIRED=1;PAIREDR=0.993665;PAO=0;PQA=0;PQR=0;PRO=0;QA=6042;QR=200372;RO=5683;RPL=91;RPP=4.27278;RPPR=7.55003;RPR=81;RUN=1;SAF=83;SAP=3.46479;SAR=89;SRF=2791;SRP=6.9081;SRR=2892;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18901A>G|p.Lys6301Glu|18901/21291|18901/21291|6301/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1126A>G|p.Lys376Glu|1126/1581|1126/1581|376/526||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2398A>G|||||2398|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-456A>G|||||456|WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1494A>G|||||1494|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2929A>G|||||2929|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1126A>G|||||1126|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5857:5683,172:5683:200372:172:6042:0,-1250.18,-16760.4
NC_045512.2	19220	.	C	T	83946.5	.	AB=0.650573;ABP=1067.61;AC=1;AF=0.5;AN=2;AO=3517;CIGAR=1X;DP=5406;DPB=5406;DPRA=0;EPP=3.08501;EPPR=3.47085;GTI=0;LEN=1;MEANALT=3;MQM=48.9795;MQMR=51.3181;NS=1;NUMALT=1;ODDS=8974.42;PAIRED=0.997157;PAIREDR=0.993107;PAO=0;PQA=0;PQR=0;PRO=0;QA=123592;QR=66525;RO=1886;RPL=1966;RPP=109.346;RPPR=12.3363;RPR=1551;RUN=1;SAF=1746;SAP=3.39619;SAR=1771;SRF=945;SRP=3.02872;SRR=941;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18956C>T|p.Ala6319Val|18956/21291|18956/21291|6319/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1181C>T|p.Ala394Val|1181/1581|1181/1581|394/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2343C>T|||||2343|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-401C>T|||||401|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1439C>T|||||1439|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*2984C>T|||||2984|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1181C>T|||||1181|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:5406:1886,3517:1886:66525:3517:123592:-8523.51,0,-4016.27
NC_045512.2	19245	.	C	T	7.03964E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=399;CIGAR=1X;DP=5068;DPB=5068;DPRA=0;EPP=3.27697;EPPR=11.8692;GTI=0;LEN=1;MEANALT=2;MQM=46.4637;MQMR=49.5467;NS=1;NUMALT=1;ODDS=3051.2;PAIRED=1;PAIREDR=0.995073;PAO=0;PQA=0;PQR=0;PRO=0;QA=14080;QR=164853;RO=4668;RPL=190;RPP=4.97497;RPPR=471.922;RPR=209;RUN=1;SAF=204;SAP=3.45113;SAR=195;SRF=2293;SRP=6.13819;SRR=2375;TYPE=snp;ANN=T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.18981C>T|p.Asp6327Asp|18981/21291|18981/21291|6327/7096||,T|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1206C>T|p.Asp402Asp|1206/1581|1206/1581|402/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2318C>T|||||2318|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-376C>T|||||376|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1414C>T|||||1414|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3009C>T|||||3009|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1206C>T|||||1206|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5068:4668,399:4668:164853:399:14080:0,-398.339,-12557.8
NC_045512.2	19333	.	G	T	18125.6	.	AB=0.270052;ABP=1875.49;AC=1;AF=0.5;AN=2;AO=1101;CIGAR=1X;DP=4077;DPB=4077;DPRA=0;EPP=4.05363;EPPR=4.17776;GTI=0;LEN=1;MEANALT=1;MQM=51.0427;MQMR=53.038;NS=1;NUMALT=1;ODDS=4173.56;PAIRED=0.998183;PAIREDR=0.996304;PAO=0;PQA=0;PQR=0;PRO=0;QA=38316;QR=104017;RO=2976;RPL=524;RPP=8.55041;RPPR=31.6159;RPR=577;RUN=1;SAF=565;SAP=4.66898;SAR=536;SRF=1491;SRP=3.03657;SRR=1485;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19069G>T|p.Asp6357Tyr|19069/21291|19069/21291|6357/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1294G>T|p.Asp432Tyr|1294/1581|1294/1581|432/526||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2230G>T|||||2230|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-288G>T|||||288|WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1326G>T|||||1326|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3097G>T|||||3097|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1294G>T|||||1294|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4077:2976,1101:2976:104017:1101:38316:-2016.57,0,-7824.46
NC_045512.2	19452	.	T	A	3.9056E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=42;CIGAR=1X;DP=3420;DPB=3420;DPRA=0;EPP=3.0103;EPPR=5.3286;GTI=0;LEN=1;MEANALT=2;MQM=47.9048;MQMR=52.6652;NS=1;NUMALT=1;ODDS=4274.34;PAIRED=0.952381;PAIREDR=0.993179;PAO=0;PQA=0;PQR=0;PRO=0;QA=1464;QR=116982;RO=3372;RPL=42;RPP=94.2121;RPPR=206.405;RPR=0;RUN=1;SAF=21;SAP=3.0103;SAR=21;SRF=1689;SRP=3.03348;SRR=1683;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19188T>A|p.Ala6396Ala|19188/21291|19188/21291|6396/7096||,A|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding|1/1|c.1413T>A|p.Ala471Ala|1413/1581|1413/1581|471/526||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-2111T>A|||||2111|,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.-169T>A|||||169|WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-1207T>A|||||1207|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3216T>A|||||3216|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1413T>A|||||1413|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3420:3372,42:3372:116982:42:1464:0,-909.276,-9987.69
NC_045512.2	19751	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=917;DPB=917;DPRA=0;EPP=3.0103;EPPR=3.09677;GTI=0;LEN=1;MEANALT=2;MQM=40.5833;MQMR=53.469;NS=1;NUMALT=1;ODDS=1151.16;PAIRED=0.833333;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=424;QR=32022;RO=904;RPL=0;RPP=29.068;RPPR=3.3562;RPR=12;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=445;SRP=3.48111;SRR=459;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19487A>T|p.Glu6496Val|19487/21291|19487/21291|6496/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.131A>T|p.Glu44Val|131/1038|131/1038|44/345||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1812A>T|||||1812|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-908A>T|||||908|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3515A>T|||||3515|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1712A>T|||||1712|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*131A>T|||||131|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:917:904,12:904:32022:12:424:0,-244.122,-2771.61
NC_045512.2	19887	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=1166;DPB=1166;DPRA=0;EPP=3.0761;EPPR=3.56419;GTI=0;LEN=1;MEANALT=1;MQM=43.4242;MQMR=51.2604;NS=1;NUMALT=1;ODDS=1295.27;PAIRED=1;PAIREDR=0.993822;PAO=0;PQA=0;PQR=0;PRO=0;QA=1115;QR=39736;RO=1133;RPL=27;RPP=32.0291;RPPR=52.6897;RPR=6;RUN=1;SAF=16;SAP=3.0761;SAR=17;SRF=563;SRP=3.10421;SRR=570;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19623A>G|p.Lys6541Lys|19623/21291|19623/21291|6541/7096||,G|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.267A>G|p.Lys89Lys|267/1038|267/1038|89/345||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1676A>G|||||1676|,G|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-772A>G|||||772|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3651A>G|||||3651|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1848A>G|||||1848|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*267A>G|||||267|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1166:1133,33:1133:39736:33:1115:0,-267.97,-3332.94
NC_045512.2	19895	.	C	T	2.14568E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=18;CIGAR=1X;DP=1174;DPB=1174;DPRA=0;EPP=3.0103;EPPR=3.689;GTI=0;LEN=1;MEANALT=2;MQM=43.0556;MQMR=51.1619;NS=1;NUMALT=1;ODDS=1425.78;PAIRED=1;PAIREDR=0.995671;PAO=0;PQA=0;PQR=0;PRO=0;QA=648;QR=40523;RO=1155;RPL=10;RPP=3.49285;RPPR=8.69749;RPR=8;RUN=1;SAF=9;SAP=3.0103;SAR=9;SRF=579;SRP=3.02722;SRR=576;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19631C>T|p.Ala6544Val|19631/21291|19631/21291|6544/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.275C>T|p.Ala92Val|275/1038|275/1038|92/345||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1668C>T|||||1668|,T|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-764C>T|||||764|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3659C>T|||||3659|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1856C>T|||||1856|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*275C>T|||||275|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1174:1155,18:1155:40523:18:648:0,-301.243,-3421.08
NC_045512.2	19983	.	CTTTTTTGA	CTTTTTGA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=24;CIGAR=1M1D7M;DP=941;DPB=938.667;DPRA=0;EPP=3.0103;EPPR=3.12892;GTI=0;LEN=1;MEANALT=11;MQM=48.125;MQMR=53.5095;NS=1;NUMALT=1;ODDS=1022.39;PAIRED=1;PAIREDR=0.994426;PAO=0.5;PQA=7;PQR=7;PRO=0.5;QA=783;QR=31500;RO=897;RPL=18;RPP=16.0391;RPPR=3.88421;RPR=6;RUN=1;SAF=12;SAP=3.0103;SAR=12;SRF=461;SRP=4.52331;SRR=436;TYPE=del;ANN=CTTTTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19725delT|p.Phe6575fs|19725/21291|19725/21291|6575/7096||,CTTTTTGA|frameshift_variant|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.369delT|p.Phe123fs|369/1038|369/1038|123/345||WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTGA|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1574delT|||||1574|,CTTTTTGA|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-670delT|||||670|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3753delT|||||3753|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*1950delT|||||1950|WARNING_TRANSCRIPT_NO_START_CODON,CTTTTTGA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*369delT|||||369|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF1ab|GU280_gp01|28|0.07)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:941:897,24:897:31500:24:783:0,-208.308,-2690.68
NC_045512.2	20088	.	T	C	5.90698E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=976;DPB=976;DPRA=0;EPP=3.0103;EPPR=3.09122;GTI=0;LEN=1;MEANALT=1;MQM=37.6;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1253.65;PAIRED=1;PAIREDR=0.995859;PAO=0;PQA=0;PQR=0;PRO=0;QA=352;QR=33724;RO=966;RPL=10;RPP=24.725;RPPR=10.0597;RPR=0;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=489;SRP=3.334;SRR=477;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.19824T>C|p.Gly6608Gly|19824/21291|19824/21291|6608/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.468T>C|p.Gly156Gly|468/1038|468/1038|156/345||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-1475T>C|||||1475|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-571T>C|||||571|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*3852T>C|||||3852|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2049T>C|||||2049|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*468T>C|||||468|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:976:966,10:966:33724:10:352:0,-267.733,-2905.83
NC_045512.2	20633	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=166;CIGAR=1X;DP=2089;DPB=2089;DPRA=0;EPP=4.31842;EPPR=3.71606;GTI=0;LEN=1;MEANALT=1;MQM=48.7711;MQMR=53.5315;NS=1;NUMALT=1;ODDS=1244.15;PAIRED=1;PAIREDR=0.9948;PAO=0;PQA=0;PQR=0;PRO=0;QA=5737;QR=67701;RO=1923;RPL=103;RPP=23.9402;RPPR=24.2045;RPR=63;RUN=1;SAF=81;SAP=3.2196;SAR=85;SRF=961;SRP=3.01143;SRR=962;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20369T>C|p.Val6790Ala|20369/21291|20369/21291|6790/7096||,C|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding|1/1|c.1013T>C|p.Val338Ala|1013/1038|1013/1038|338/345||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-930T>C|||||930|,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4760T>C|||||4760|,C|upstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.-26T>C|||||26|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4397T>C|||||4397|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2594T>C|||||2594|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1013T>C|||||1013|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2089:1923,166:1923:67701:166:5737:0,-153.829,-5451.28
NC_045512.2	20686	.	G	A	4.91807E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=36;CIGAR=1X;DP=1937;DPB=1937;DPRA=0;EPP=3.0103;EPPR=3.06627;GTI=0;LEN=1;MEANALT=1;MQM=47.8333;MQMR=53.9274;NS=1;NUMALT=1;ODDS=2289.62;PAIRED=1;PAIREDR=0.99474;PAO=0;PQA=0;PQR=0;PRO=0;QA=1232;QR=66116;RO=1901;RPL=12;RPP=11.6962;RPPR=11.6562;RPR=24;RUN=1;SAF=18;SAP=3.0103;SAR=18;SRF=941;SRP=3.42266;SRR=960;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20422G>A|p.Ala6808Thr|20422/21291|20422/21291|6808/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.28G>A|p.Ala10Thr|28/894|28/894|10/297||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-877G>A|||||877|,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4707G>A|||||4707|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4450G>A|||||4450|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2647G>A|||||2647|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1066G>A|||||1066|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*28G>A|||||28|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1937:1901,36:1901:66116:36:1232:0,-482.402,-5715.89
NC_045512.2	20897	.	C	A	4.32142E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=1649;DPB=1649;DPRA=0;EPP=3.22745;EPPR=4.1453;GTI=0;LEN=1;MEANALT=1;MQM=47.125;MQMR=51.7551;NS=1;NUMALT=1;ODDS=1885.05;PAIRED=1;PAIREDR=0.986948;PAO=0;PQA=0;PQR=0;PRO=0;QA=1318;QR=55575;RO=1609;RPL=16;RPP=6.48466;RPPR=13.2253;RPR=24;RUN=1;SAF=23;SAP=4.96463;SAR=17;SRF=814;SRP=3.4975;SRR=795;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20633C>A|p.Pro6878Gln|20633/21291|20633/21291|6878/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.239C>A|p.Pro80Gln|239/894|239/894|80/297||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-666C>A|||||666|,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4496C>A|||||4496|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4661C>A|||||4661|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2858C>A|||||2858|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1277C>A|||||1277|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*239C>A|||||239|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1649:1609,40:1609:55575:40:1318:0,-397.579,-4648.18
NC_045512.2	20912	.	T	A	1.13313E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1786;DPB=1786;DPRA=0;EPP=3.0103;EPPR=3.60678;GTI=0;LEN=1;MEANALT=2;MQM=32.05;MQMR=51.4484;NS=1;NUMALT=1;ODDS=2291.88;PAIRED=0.7;PAIREDR=0.988082;PAO=0;PQA=0;PQR=0;PRO=0;QA=694;QR=62244;RO=1762;RPL=0;RPP=46.4397;RPPR=4.11945;RPR=20;RUN=1;SAF=10;SAP=3.0103;SAR=10;SRF=902;SRP=5.18424;SRR=860;TYPE=snp;ANN=A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20648T>A|p.Leu6883*|20648/21291|20648/21291|6883/7096||,A|stop_gained|HIGH|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.254T>A|p.Leu85*|254/894|254/894|85/297||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-651T>A|||||651|,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4481T>A|||||4481|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4676T>A|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2873T>A|||||2873|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1292T>A|||||1292|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*254T>A|||||254|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1786:1762,20:1762:62244:20:694:0,-495.972,-5248.21
NC_045512.2	21004	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=2194;DPB=2194;DPRA=0;EPP=3.52123;EPPR=3.93042;GTI=0;LEN=1;MEANALT=2;MQM=51.5882;MQMR=52.7298;NS=1;NUMALT=1;ODDS=2307.07;PAIRED=1;PAIREDR=0.989171;PAO=0;PQA=0;PQR=0;PRO=0;QA=2334;QR=73971;RO=2124;RPL=21;RPP=24.5973;RPPR=17.7321;RPR=47;RUN=1;SAF=35;SAP=3.13803;SAR=33;SRF=1065;SRP=3.0471;SRR=1059;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20740G>T|p.Ala6914Ser|20740/21291|20740/21291|6914/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.346G>T|p.Ala116Ser|346/894|346/894|116/297||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-559G>T|||||559|,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4389G>T|||||4389|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4768G>T|||||4768|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*2965G>T|||||2965|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1384G>T|||||1384|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*346G>T|||||346|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2194:2124,68:2124:73971:68:2334:0,-465.125,-6190.18
NC_045512.2	21137	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=62;CIGAR=1X;DP=3005;DPB=3005;DPRA=0;EPP=3.15039;EPPR=15.2971;GTI=0;LEN=1;MEANALT=2;MQM=48.9839;MQMR=50.9398;NS=1;NUMALT=1;ODDS=3469.52;PAIRED=1;PAIREDR=0.991159;PAO=0;PQA=0;PQR=0;PRO=0;QA=2198;QR=103359;RO=2941;RPL=10;RPP=64.7922;RPPR=102.457;RPR=52;RUN=1;SAF=32;SAP=3.15039;SAR=30;SRF=1478;SRP=3.17643;SRR=1463;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.20873A>G|p.Lys6958Arg|20873/21291|20873/21291|6958/7096||,G|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.479A>G|p.Lys160Arg|479/894|479/894|160/297||WARNING_TRANSCRIPT_NO_START_CODON,G|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-426A>G|||||426|,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4256A>G|||||4256|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725307.1|protein_coding||c.*4901A>G|||||4901|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3098A>G|||||3098|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1517A>G|||||1517|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*479A>G|||||479|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3005:2941,62:2941:103359:62:2198:0,-720.982,-8572.97
NC_045512.2	21357	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=76;CIGAR=1X;DP=3104;DPB=3104;DPRA=0;EPP=3.46745;EPPR=3.74513;GTI=0;LEN=1;MEANALT=2;MQM=49.4211;MQMR=50.8596;NS=1;NUMALT=1;ODDS=3454.76;PAIRED=0.973684;PAIREDR=0.954726;PAO=0;PQA=0;PQR=0;PRO=0;QA=2692;QR=107210;RO=3026;RPL=35;RPP=4.03889;RPPR=55.3237;RPR=41;RUN=1;SAF=37;SAP=3.12459;SAR=39;SRF=1503;SRP=3.29734;SRR=1523;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21093T>C|p.Asn7031Asn|21093/21291|21093/21291|7031/7096||,C|synonymous_variant|LOW|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.699T>C|p.Asn233Asn|699/894|699/894|233/297||WARNING_TRANSCRIPT_NO_START_CODON,C|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-206T>C|||||206|,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-4036T>C|||||4036|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4888T>C|||||4888|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3318T>C|||||3318|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1737T>C|||||1737|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*699T>C|||||699|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3104:3026,76:3026:107210:76:2692:0,-714.996,-8823.97
NC_045512.2	21408	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=33;CIGAR=1X;DP=3187;DPB=3187;DPRA=0;EPP=3.0761;EPPR=14.653;GTI=0;LEN=1;MEANALT=2;MQM=42.0303;MQMR=50.2262;NS=1;NUMALT=1;ODDS=4058.01;PAIRED=0.909091;PAIREDR=0.961294;PAO=0;PQA=0;PQR=0;PRO=0;QA=1172;QR=111449;RO=3152;RPL=24;RPP=17.8158;RPPR=4.87314;RPR=9;RUN=1;SAF=15;SAP=3.60252;SAR=18;SRF=1597;SRP=4.22555;SRR=1555;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21144T>A|p.Phe7048Leu|21144/21291|21144/21291|7048/7096||,A|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.750T>A|p.Phe250Leu|750/894|750/894|250/297||WARNING_TRANSCRIPT_NO_START_CODON,A|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-155T>A|||||155|,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3985T>A|||||3985|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4837T>A|||||4837|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3369T>A|||||3369|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1788T>A|||||1788|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*750T>A|||||750|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3187:3152,33:3152:111449:33:1172:0,-876.049,-9303.39
NC_045512.2	21417	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3209;DPB=3209;DPRA=0;EPP=3.54779;EPPR=9.44926;GTI=0;LEN=1;MEANALT=1;MQM=44.9208;MQMR=49.8475;NS=1;NUMALT=1;ODDS=3401.21;PAIRED=0.960396;PAIREDR=0.95045;PAO=0;PQA=0;PQR=0;PRO=0;QA=3474;QR=109181;RO=3108;RPL=70;RPP=35.7114;RPPR=41.2668;RPR=31;RUN=1;SAF=47;SAP=4.06379;SAR=54;SRF=1571;SRP=3.81796;SRR=1537;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding|2/2|c.21153A>T|p.Lys7051Asn|21153/21291|21153/21291|7051/7096||,T|missense_variant|MODERATE|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding|1/1|c.759A>T|p.Lys253Asn|759/894|759/894|253/297||WARNING_TRANSCRIPT_NO_START_CODON,T|upstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.-146A>T|||||146|,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3976A>T|||||3976|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4828A>T|||||4828|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3378A>T|||||3378|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1797A>T|||||1797|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*759A>T|||||759|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3209:3108,101:3108:109181:101:3474:0,-695.817,-8846.14
NC_045512.2	21575	.	C	T	4774.91	.	AB=0.206853;ABP=1767.56;AC=1;AF=0.5;AN=2;AO=489;CIGAR=1X;DP=2364;DPB=2364;DPRA=0;EPP=3.01474;EPPR=3.27143;GTI=0;LEN=1;MEANALT=3;MQM=47.4703;MQMR=52.6018;NS=1;NUMALT=1;ODDS=1099.46;PAIRED=1;PAIREDR=0.99519;PAO=0;PQA=0;PQR=0;PRO=0;QA=17184;QR=65447;RO=1871;RPL=279;RPP=24.1522;RPPR=8.22021;RPR=210;RUN=1;SAF=242;SAP=3.12132;SAR=247;SRF=936;SRP=3.01146;SRR=935;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.13C>T|p.Leu5Phe|13/3822|13/3822|5/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3818C>T|||||3818|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4670C>T|||||4670|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4948C>T|||||4948|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*20C>T|||||20|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3536C>T|||||3536|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1955C>T|||||1955|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*917C>T|||||917|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*23C>T|||||23|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2364:1871,489:1871:65447:489:17184:-675.122,0,-4947.91
NC_045512.2	21618	.	C	G	35360.1	.	AB=0.703596;ABP=743.974;AC=1;AF=0.5;AN=2;AO=1448;CIGAR=1X;DP=2058;DPB=2058;DPRA=0;EPP=3.0103;EPPR=3.01387;GTI=0;LEN=1;MEANALT=2;MQM=50.1657;MQMR=52.7011;NS=1;NUMALT=1;ODDS=2619.29;PAIRED=0.998619;PAIREDR=0.996716;PAO=0;PQA=0;PQR=0;PRO=0;QA=50596;QR=21344;RO=609;RPL=790;RPP=29.14;RPPR=25.2634;RPR=658;RUN=1;SAF=688;SAP=10.7844;SAR=760;SRF=298;SRP=3.61289;SRR=311;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.56C>G|p.Thr19Arg|56/3822|56/3822|19/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3775C>G|||||3775|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4627C>G|||||4627|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4905C>G|||||4905|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*63C>G|||||63|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3579C>G|||||3579|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*1998C>G|||||1998|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*960C>G|||||960|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*66C>G|||||66|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2058:609,1448:609:21344:1448:50596:-3624.67,0,-1224.54
NC_045512.2	21650	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=198;CIGAR=1X;DP=1834;DPB=1834;DPRA=0;EPP=4.58955;EPPR=5.81888;GTI=0;LEN=1;MEANALT=1;MQM=45.2424;MQMR=51.4438;NS=1;NUMALT=1;ODDS=807.489;PAIRED=1;PAIREDR=0.997555;PAO=0;PQA=0;PQR=0;PRO=0;QA=6993;QR=57736;RO=1636;RPL=198;RPP=432.962;RPPR=3.27045;RPR=0;RUN=1;SAF=93;SAP=4.58955;SAR=105;SRF=794;SRP=6.06841;SRR=842;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.88A>C|p.Asn30His|88/3822|88/3822|30/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3743A>C|||||3743|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4595A>C|||||4595|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4873A>C|||||4873|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*95A>C|||||95|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3611A>C|||||3611|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2030A>C|||||2030|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*992A>C|||||992|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*98A>C|||||98|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1834:1636,198:1636:57736:198:6993:0,-5.24931,-4377.3
NC_045512.2	21656	.	TTCACACG	TACC	6.46099E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=51;CIGAR=1M4D2M1X;DP=1573;DPB=1546.88;DPRA=0;EPP=5.09662;EPPR=5.44218;GTI=0;LEN=4;MEANALT=13;MQM=45.3333;MQMR=51.4031;NS=1;NUMALT=1;ODDS=1644.42;PAIRED=1;PAIREDR=0.997335;PAO=0;PQA=0;PQR=0;PRO=0;QA=1783;QR=52647;RO=1501;RPL=51;RPP=113.755;RPPR=24.1912;RPR=0;RUN=1;SAF=22;SAP=5.09662;SAR=29;SRF=731;SRP=5.21071;SRR=770;TYPE=complex;ANN=ACC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.95_101delTCACACGinsACC|p.Phe32fs|95/3822|95/3822|32/1273||,ACC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3736_-3730delTCACACGinsACC|||||3736|,ACC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4588_-4582delTCACACGinsACC|||||4588|,ACC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4866_-4860delTCACACGinsACC|||||4866|,ACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*102_*108delTCACACGinsACC|||||102|,ACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3618_*3624delTCACACGinsACC|||||3618|WARNING_TRANSCRIPT_NO_START_CODON,ACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2037_*2043delTCACACGinsACC|||||2037|WARNING_TRANSCRIPT_NO_START_CODON,ACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*999_*1005delTCACACGinsACC|||||999|WARNING_TRANSCRIPT_NO_START_CODON,ACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*105_*111delTCACACGinsACC|||||105|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1573:1501,51:1501:52647:51:1783:0,-323.476,-4349.96
NC_045512.2	21764	.	ATACATGT	AT	20265.8	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=744;CIGAR=1M6D1M;DP=744;DPB=186.75;DPRA=0;EPP=6.38425;EPPR=0;GTI=0;LEN=6;MEANALT=1;MQM=49.7083;MQMR=0;NS=1;NUMALT=1;ODDS=1036.01;PAIRED=0.995968;PAIREDR=0;PAO=3;PQA=0;PQR=0;PRO=3;QA=24386;QR=0;RO=0;RPL=373;RPP=3.02197;RPPR=0;RPR=371;RUN=1;SAF=378;SAP=3.43058;SAR=366;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=AT|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.204_209delACATGT|p.His69_Val70del|204/3822|204/3822|68/1273||,AT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3627_-3622delACATGT|||||3627|,AT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4479_-4474delACATGT|||||4479|,AT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4757_-4752delACATGT|||||4757|,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*211_*216delACATGT|||||211|,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3727_*3732delACATGT|||||3727|WARNING_TRANSCRIPT_NO_START_CODON,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2146_*2151delACATGT|||||2146|WARNING_TRANSCRIPT_NO_START_CODON,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1108_*1113delACATGT|||||1108|WARNING_TRANSCRIPT_NO_START_CODON,AT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*214_*219delACATGT|||||214|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:744:0,744:0:0:744:24386:-2031.56,-223.966,0
NC_045512.2	21855	.	C	T	10363.6	.	AB=0.552296;ABP=21.634;AC=1;AF=0.5;AN=2;AO=433;CIGAR=1X;DP=784;DPB=784;DPRA=0;EPP=3.05543;EPPR=3.16496;GTI=0;LEN=1;MEANALT=1;MQM=50.321;MQMR=52.8519;NS=1;NUMALT=1;ODDS=1907.65;PAIRED=0.995381;PAIREDR=0.997151;PAO=0;PQA=0;PQR=0;PRO=0;QA=15293;QR=12291;RO=351;RPL=218;RPP=3.05543;RPPR=4.79821;RPR=215;RUN=1;SAF=222;SAP=3.61711;SAR=211;SRF=176;SRP=3.01649;SRR=175;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.293C>T|p.Ser98Phe|293/3822|293/3822|98/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3538C>T|||||3538|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4390C>T|||||4390|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4668C>T|||||4668|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*300C>T|||||300|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3816C>T|||||3816|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2235C>T|||||2235|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1197C>T|||||1197|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*303C>T|||||303|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:784:351,433:351:12291:433:15293:-1046.09,0,-838.198
NC_045512.2	21974	.	G	C	6907.42	.	AB=0.470907;ABP=8.44339;AC=1;AF=0.5;AN=2;AO=348;CIGAR=1X;DP=739;DPB=739;DPRA=0;EPP=3.40965;EPPR=3.21074;GTI=0;LEN=1;MEANALT=2;MQM=43.75;MQMR=45.7;NS=1;NUMALT=1;ODDS=1590.49;PAIRED=1;PAIREDR=0.94359;PAO=0;PQA=0;PQR=0;PRO=0;QA=12325;QR=13699;RO=390;RPL=257;RPP=174.956;RPPR=8.02139;RPR=91;RUN=1;SAF=169;SAP=3.63429;SAR=179;SRF=196;SRP=3.03257;SRR=194;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.412G>C|p.Asp138His|412/3822|412/3822|138/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3419G>C|||||3419|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4271G>C|||||4271|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4549G>C|||||4549|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*419G>C|||||419|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3935G>C|||||3935|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2354G>C|||||2354|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1316G>C|||||1316|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*422G>C|||||422|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:739:390,348:390:13699:348:12325:-716.861,0,-870.869
NC_045512.2	21979	.	ATTTTTGGGTGTTTATTAC	ATTTTGGGTGTTTAC,ATTTTTGGGTGTTTAC	10664.2	.	AB=0,0;ABP=0,0;AC=0,2;AF=0,1;AN=2;AO=12,482;CIGAR=1M1D10M3D4M,12M3D4M;DP=548;DPB=469.368;DPRA=0,0;EPP=3.73412,3.65904;EPPR=3.0565;GTI=0;LEN=15,3;MEANALT=5,5;MQM=28.9167,42.9523;MQMR=43.6809;NS=1;NUMALT=2;ODDS=308.58;PAIRED=1,0.977178;PAIREDR=0.829787;PAO=0,0.5;PQA=0,12;PQR=12;PRO=0.5;QA=254,13811;QR=1634;RO=47;RPL=2,311;RPP=14.5915,91.3108;RPPR=80.6751;RPR=10,171;RUN=1,1;SAF=7,234;SAP=3.73412,3.89331;SAR=5,248;SRF=24;SRP=3.0565;SRR=23;TYPE=complex,del;ANN=GGGTGTTTAC|frameshift_variant&missense_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.422_431delTGGGTGTTTAinsGGGTGT|p.Leu141fs|422/3822|422/3822|141/1273||INFO_REALIGN_3_PRIME,ATTTTTGGGTGTTTAC|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.432_434delTTA|p.Tyr145del|432/3822|432/3822|144/1273||,GGGTGTTTAC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3409_-3396delTGGGTGTTTATTACinsGGGTGTTTAC|||||3409|,ATTTTTGGGTGTTTAC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3399_-3397delTTA|||||3399|,GGGTGTTTAC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4261_-4248delTGGGTGTTTATTACinsGGGTGTTTAC|||||4261|,ATTTTTGGGTGTTTAC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4251_-4249delTTA|||||4251|,GGGTGTTTAC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4539_-4526delTGGGTGTTTATTACinsGGGTGTTTAC|||||4539|,ATTTTTGGGTGTTTAC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4529_-4527delTTA|||||4529|,GGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*429_*442delTGGGTGTTTATTACinsGGGTGTTTAC|||||429|,ATTTTTGGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*439_*441delTTA|||||439|,GGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3945_*3958delTGGGTGTTTATTACinsGGGTGTTTAC|||||3945|WARNING_TRANSCRIPT_NO_START_CODON,ATTTTTGGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3955_*3957delTTA|||||3955|WARNING_TRANSCRIPT_NO_START_CODON,GGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2364_*2377delTGGGTGTTTATTACinsGGGTGTTTAC|||||2364|WARNING_TRANSCRIPT_NO_START_CODON,ATTTTTGGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2374_*2376delTTA|||||2374|WARNING_TRANSCRIPT_NO_START_CODON,GGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1326_*1339delTGGGTGTTTATTACinsGGGTGTTTAC|||||1326|WARNING_TRANSCRIPT_NO_START_CODON,ATTTTTGGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1336_*1338delTTA|||||1336|WARNING_TRANSCRIPT_NO_START_CODON,GGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*432_*445delTGGGTGTTTATTACinsGGGTGTTTAC|||||432|WARNING_TRANSCRIPT_NO_START_CODON,ATTTTTGGGTGTTTAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*442_*444delTTA|||||442|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	2/2:548:47,12,482:47:1634:12,482:254,13811:-1068.01,-1064.49,-1177.28,-28.6243,-127.448,0
NC_045512.2	22028	.	GAGTTCAG	GG	0.0	.	AB=0.118812;ABP=640.37;AC=1;AF=0.5;AN=2;AO=60;CIGAR=1M6D1M;DP=505;DPB=460;DPRA=0;EPP=3.58936;EPPR=11.6375;GTI=0;LEN=6;MEANALT=2;MQM=49.9;MQMR=43.2995;NS=1;NUMALT=1;ODDS=137.724;PAIRED=1;PAIREDR=0.972973;PAO=0;PQA=0;PQR=0;PRO=0;QA=1971;QR=15417;RO=444;RPL=22;RPP=12.2752;RPPR=53.8932;RPR=38;RUN=1;SAF=32;SAP=3.58936;SAR=28;SRF=208;SRP=6.84461;SRR=236;TYPE=del;ANN=GG|disruptive_inframe_deletion|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.467_472delAGTTCA|p.Glu156_Arg158delinsGly|467/3822|467/3822|156/1273||,GG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3364_-3359delAGTTCA|||||3364|,GG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4216_-4211delAGTTCA|||||4216|,GG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4494_-4489delAGTTCA|||||4494|,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*474_*479delAGTTCA|||||474|,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*3990_*3995delAGTTCA|||||3990|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2409_*2414delAGTTCA|||||2409|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1371_*1376delAGTTCA|||||1371|WARNING_TRANSCRIPT_NO_START_CODON,GG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*477_*482delAGTTCA|||||477|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:505:444,60:444:15417:60:1971:-19.2725,0,-1029.82
NC_045512.2	22070	.	T	G	2.82671E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=11;CIGAR=1X;DP=415;DPB=415;DPRA=0;EPP=3.20771;EPPR=3.2038;GTI=0;LEN=1;MEANALT=1;MQM=56.8182;MQMR=53.0619;NS=1;NUMALT=1;ODDS=464.115;PAIRED=0.909091;PAIREDR=0.992574;PAO=0;PQA=0;PQR=0;PRO=0;QA=372;QR=14318;RO=404;RPL=0;RPP=26.8965;RPPR=3.0963;RPR=11;RUN=1;SAF=5;SAP=3.20771;SAR=6;SRF=209;SRP=4.06379;SRR=195;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.508T>G|p.Tyr170Asp|508/3822|508/3822|170/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3323T>G|||||3323|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4175T>G|||||4175|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4453T>G|||||4453|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*515T>G|||||515|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4031T>G|||||4031|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2450T>G|||||2450|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1412T>G|||||1412|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*518T>G|||||518|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:415:404,11:404:14318:11:372:0,-91.1698,-1211.65
NC_045512.2	22218	.	GTTTTTCG	GTTTTCG	6.08732E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1M1D6M;DP=973;DPB=971.75;DPRA=0;EPP=3.0103;EPPR=3.15721;GTI=0;LEN=1;MEANALT=7;MQM=53.0833;MQMR=53.0095;NS=1;NUMALT=1;ODDS=1193.66;PAIRED=1;PAIREDR=0.988372;PAO=1;PQA=34;PQR=34;PRO=1;QA=406;QR=32735;RO=946;RPL=2;RPP=14.5915;RPPR=39.4525;RPR=10;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=463;SRP=3.92847;SRR=483;TYPE=del;ANN=GTTTTCG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.661delT|p.Ser221fs|661/3822|661/3822|221/1273||,GTTTTCG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3170delT|||||3170|,GTTTTCG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-4022delT|||||4022|,GTTTTCG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4300delT|||||4300|,GTTTTCG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4979delT|||||4979|,GTTTTCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*668delT|||||668|,GTTTTCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4184delT|||||4184|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2603delT|||||2603|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1565delT|||||1565|WARNING_TRANSCRIPT_NO_START_CODON,GTTTTCG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*671delT|||||671|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:973:946,12:946:32735:12:406:0,-251.995,-2798.42
NC_045512.2	22282	.	TTTACTTGCT	TT	1.8708E-13	.	AB=0.146825;ABP=2733.21;AC=1;AF=0.5;AN=2;AO=370;CIGAR=1M8D1M;DP=2520;DPB=2226.5;DPRA=0;EPP=3.03378;EPPR=34.8149;GTI=0;LEN=8;MEANALT=10;MQM=46.7216;MQMR=49.7873;NS=1;NUMALT=1;ODDS=261.116;PAIRED=0.97027;PAIREDR=0.989247;PAO=11.5;PQA=371.5;PQR=443.5;PRO=13.5;QA=11823;QR=75374;RO=2139;RPL=204;RPP=11.4849;RPPR=2756.8;RPR=166;RUN=1;SAF=176;SAP=4.91181;SAR=194;SRF=1146;SRP=26.7747;SRR=993;TYPE=del;ANN=TT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.723_730delACTTGCTT|p.Leu241fs|723/3822|723/3822|241/1273||INFO_REALIGN_3_PRIME,TT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3109_-3102delTACTTGCT|||||3109|,TT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3961_-3954delTACTTGCT|||||3961|,TT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4239_-4232delTACTTGCT|||||4239|,TT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4918_-4911delTACTTGCT|||||4918|,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*729_*736delTACTTGCT|||||729|,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4245_*4252delTACTTGCT|||||4245|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2664_*2671delTACTTGCT|||||2664|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1626_*1633delTACTTGCT|||||1626|WARNING_TRANSCRIPT_NO_START_CODON,TT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*732_*739delTACTTGCT|||||732|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2520:2139,370:2139:75374:370:11823:-194.926,0,-5543.52
NC_045512.2	22315	.	T	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=357;CIGAR=1X;DP=4311;DPB=4311;DPRA=0;EPP=3.30835;EPPR=18.922;GTI=0;LEN=1;MEANALT=3;MQM=48.1261;MQMR=49.6176;NS=1;NUMALT=1;ODDS=2556.05;PAIRED=0.985994;PAIREDR=0.992901;PAO=0;PQA=0;PQR=0;PRO=0;QA=12323;QR=138793;RO=3944;RPL=57;RPP=362.179;RPPR=1298.6;RPR=300;RUN=1;SAF=185;SAP=4.03825;SAR=172;SRF=2048;SRP=15.7308;SRR=1896;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.753T>G|p.Pro251Pro|753/3822|753/3822|251/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-3078T>G|||||3078|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3930T>G|||||3930|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-4208T>G|||||4208|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4887T>G|||||4887|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*760T>G|||||760|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4276T>G|||||4276|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2695T>G|||||2695|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1657T>G|||||1657|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*763T>G|||||763|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4311:3944,357:3944:138793:357:12323:0,-302.488,-10551.5
NC_045512.2	22600	.	ATTTGC	ATTGC	4.14663E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=275;CIGAR=1M1D4M;DP=5420;DPB=5374.17;DPRA=0;EPP=11.6093;EPPR=8.62691;GTI=0;LEN=1;MEANALT=12;MQM=50.6836;MQMR=52.2494;NS=1;NUMALT=1;ODDS=4743.11;PAIRED=1;PAIREDR=0.995893;PAO=0;PQA=0;PQR=0;PRO=0;QA=8676;QR=179526;RO=5113;RPL=253;RPP=424.363;RPPR=1086.16;RPR=22;RUN=1;SAF=121;SAP=11.6093;SAR=154;SRF=2497;SRP=9.02442;SRR=2616;TYPE=del;ANN=ATTGC|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1041delT|p.Phe347fs|1041/3822|1041/3822|347/1273||,ATTGC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2790delT|||||2790|,ATTGC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3642delT|||||3642|,ATTGC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3920delT|||||3920|,ATTGC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4599delT|||||4599|,ATTGC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4791delT|||||4791|,ATTGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1048delT|||||1048|,ATTGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4564delT|||||4564|WARNING_TRANSCRIPT_NO_START_CODON,ATTGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*2983delT|||||2983|WARNING_TRANSCRIPT_NO_START_CODON,ATTGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1945delT|||||1945|WARNING_TRANSCRIPT_NO_START_CODON,ATTGC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1051delT|||||1051|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5420:5113,275:5113:179526:275:8676:0,-851.108,-14682.4
NC_045512.2	22643	.	TGT	ACA	1.12947E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=3X;DP=3250;DPB=3250;DPRA=0;EPP=3.1419;EPPR=4.04925;GTI=0;LEN=3;MEANALT=3;MQM=42.2879;MQMR=53.4939;NS=1;NUMALT=1;ODDS=3785.89;PAIRED=0.924242;PAIREDR=0.996854;PAO=0;PQA=0;PQR=0;PRO=0;QA=2317;QR=110756;RO=3179;RPL=27;RPP=7.74806;RPPR=167.685;RPR=39;RUN=1;SAF=31;SAP=3.53672;SAR=35;SRF=1582;SRP=3.16399;SRR=1597;TYPE=complex;ANN=ACA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1081_1083delTGTinsACA|p.Cys361Thr|1081/3822|1081/3822|361/1273||,ACA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2750_-2748delTGTinsACA|||||2750|,ACA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3602_-3600delTGTinsACA|||||3602|,ACA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3880_-3878delTGTinsACA|||||3880|,ACA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4559_-4557delTGTinsACA|||||4559|,ACA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4751_-4749delTGTinsACA|||||4751|,ACA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1088_*1090delTGTinsACA|||||1088|,ACA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4604_*4606delTGTinsACA|||||4604|WARNING_TRANSCRIPT_NO_START_CODON,ACA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3023_*3025delTGTinsACA|||||3023|WARNING_TRANSCRIPT_NO_START_CODON,ACA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*1985_*1987delTGTinsACA|||||1985|WARNING_TRANSCRIPT_NO_START_CODON,ACA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1091_*1093delTGTinsACA|||||1091|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3250:3179,66:3179:110756:66:2317:0,-800.501,-9497.37
NC_045512.2	22852	.	A	G	0.0	.	AB=0.143746;ABP=3193.32;AC=1;AF=0.5;AN=2;AO=416;CIGAR=1X;DP=2894;DPB=2894;DPRA=0;EPP=5.09825;EPPR=10.6047;GTI=0;LEN=1;MEANALT=3;MQM=43.2572;MQMR=50.5285;NS=1;NUMALT=1;ODDS=362.403;PAIRED=1;PAIREDR=0.984634;PAO=0;PQA=0;PQR=0;PRO=0;QA=14466;QR=87462;RO=2473;RPL=335;RPP=339.776;RPPR=45.1235;RPR=81;RUN=1;SAF=199;SAP=4.70154;SAR=217;SRF=1207;SRP=6.06687;SRR=1266;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1290A>G|p.Thr430Thr|1290/3822|1290/3822|430/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2541A>G|||||2541|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3393A>G|||||3393|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3671A>G|||||3671|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4350A>G|||||4350|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4542A>G|||||4542|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4904A>G|||||4904|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1297A>G|||||1297|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4813A>G|||||4813|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3232A>G|||||3232|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2194A>G|||||2194|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1300A>G|||||1300|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2894:2473,416:2473:87462:416:14466:-239.51,0,-6540.23
NC_045512.2	22917	.	T	G	25609.5	.	AB=0.654307;ABP=365.559;AC=1;AF=0.5;AN=2;AO=1147;CIGAR=1X;DP=1753;DPB=1753;DPRA=0;EPP=5.88982;EPPR=3.93066;GTI=0;LEN=1;MEANALT=2;MQM=49.0113;MQMR=53.3858;NS=1;NUMALT=1;ODDS=2887.26;PAIRED=0.975588;PAIREDR=0.993377;PAO=0;PQA=0;PQR=0;PRO=0;QA=37925;QR=20944;RO=604;RPL=580;RPP=3.33025;RPPR=3.71495;RPR=567;RUN=1;SAF=582;SAP=3.55743;SAR=565;SRF=309;SRP=3.71495;SRR=295;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1355T>G|p.Leu452Arg|1355/3822|1355/3822|452/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2476T>G|||||2476|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3328T>G|||||3328|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3606T>G|||||3606|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4285T>G|||||4285|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4477T>G|||||4477|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4839T>G|||||4839|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4977T>G|||||4977|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1362T>G|||||1362|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4878T>G|||||4878|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3297T>G|||||3297|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2259T>G|||||2259|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1365T>G|||||1365|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1753:604,1147:604:20944:1147:37925:-2607.08,0,-1299.49
NC_045512.2	22995	.	C	A	26960.9	.	AB=0.637002;ABP=281.467;AC=1;AF=0.5;AN=2;AO=1088;CIGAR=1X;DP=1708;DPB=1708;DPRA=0;EPP=3.13803;EPPR=3.79961;GTI=0;LEN=1;MEANALT=2;MQM=50.7574;MQMR=53.2084;NS=1;NUMALT=1;ODDS=3085.5;PAIRED=0.988051;PAIREDR=0.996769;PAO=0;PQA=0;PQR=0;PRO=0;QA=38250;QR=21584;RO=619;RPL=537;RPP=3.40148;RPPR=4.02412;RPR=551;RUN=1;SAF=541;SAP=3.08215;SAR=547;SRF=306;SRP=3.18219;SRR=313;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1433C>A|p.Thr478Lys|1433/3822|1433/3822|478/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2398C>A|||||2398|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3250C>A|||||3250|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3528C>A|||||3528|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4207C>A|||||4207|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4399C>A|||||4399|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4761C>A|||||4761|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4899C>A|||||4899|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1440C>A|||||1440|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725308.1|protein_coding||c.*4956C>A|||||4956|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3375C>A|||||3375|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2337C>A|||||2337|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1443C>A|||||1443|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1708:619,1088:619:21584:1088:38250:-2733.04,0,-1376.73
NC_045512.2	23063	.	A	T	11471.4	.	AB=0.363065;ABP=262.299;AC=1;AF=0.5;AN=2;AO=578;CIGAR=1X;DP=1592;DPB=1592;DPRA=0;EPP=3.0103;EPPR=3.55852;GTI=0;LEN=1;MEANALT=1;MQM=48.7907;MQMR=51.641;NS=1;NUMALT=1;ODDS=2641.38;PAIRED=0.989619;PAIREDR=0.97929;PAO=0;PQA=0;PQR=0;PRO=0;QA=20314;QR=35139;RO=1014;RPL=301;RPP=5.17426;RPPR=3.31867;RPR=277;RUN=1;SAF=288;SAP=3.02533;SAR=290;SRF=504;SRP=3.08739;SRR=510;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1501A>T|p.Asn501Tyr|1501/3822|1501/3822|501/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2330A>T|||||2330|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-3182A>T|||||3182|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3460A>T|||||3460|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-4139A>T|||||4139|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4331A>T|||||4331|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4693A>T|||||4693|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4831A>T|||||4831|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1508A>T|||||1508|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3443A>T|||||3443|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2405A>T|||||2405|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1511A>T|||||1511|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1592:1014,578:1014:35139:578:20314:-1181.74,0,-2507.13
NC_045512.2	23271	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=99;CIGAR=1X;DP=3990;DPB=3990;DPRA=0;EPP=3.03223;EPPR=3.54827;GTI=0;LEN=1;MEANALT=2;MQM=47.1616;MQMR=52.3784;NS=1;NUMALT=1;ODDS=4435.23;PAIRED=1;PAIREDR=0.998453;PAO=0;PQA=0;PQR=0;PRO=0;QA=3411;QR=135408;RO=3879;RPL=40;RPP=10.9285;RPPR=125.097;RPR=59;RUN=1;SAF=50;SAP=3.03223;SAR=49;SRF=1984;SRP=7.44449;SRR=1895;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1709C>A|p.Ala570Asp|1709/3822|1709/3822|570/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2122C>A|||||2122|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2974C>A|||||2974|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3252C>A|||||3252|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3931C>A|||||3931|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4123C>A|||||4123|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4485C>A|||||4485|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4623C>A|||||4623|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1716C>A|||||1716|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3651C>A|||||3651|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2613C>A|||||2613|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1719C>A|||||1719|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3990:3879,99:3879:135408:99:3411:0,-922.477,-11401.5
NC_045512.2	23302	.	G	C	1478.84	.	AB=0.154267;ABP=4370.88;AC=1;AF=0.5;AN=2;AO=649;CIGAR=1X;DP=4207;DPB=4207;DPRA=0;EPP=3.97726;EPPR=3.89208;GTI=0;LEN=1;MEANALT=2;MQM=50.0555;MQMR=53.4027;NS=1;NUMALT=1;ODDS=340.516;PAIRED=0.996918;PAIREDR=0.996625;PAO=0;PQA=0;PQR=0;PRO=0;QA=22618;QR=125381;RO=3556;RPL=295;RPP=14.6573;RPPR=18.2546;RPR=354;RUN=1;SAF=323;SAP=3.04041;SAR=326;SRF=1770;SRP=3.16663;SRR=1786;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1740G>C|p.Gln580His|1740/3822|1740/3822|580/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-2091G>C|||||2091|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2943G>C|||||2943|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3221G>C|||||3221|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3900G>C|||||3900|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-4092G>C|||||4092|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4454G>C|||||4454|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4592G>C|||||4592|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4972G>C|||||4972|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1747G>C|||||1747|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3682G>C|||||3682|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2644G>C|||||2644|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1750G>C|||||1750|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4207:3556,649:3556:125381:649:22618:-637.692,0,-9696.8
NC_045512.2	23403	.	A	G	104667.0	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3570;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=4.29737;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=50.3319;MQMR=54;NS=1;NUMALT=1;ODDS=4927.87;PAIRED=0.995798;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=124700;QR=72;RO=2;RPL=1945;RPP=65.2957;RPPR=7.35324;RPR=1625;RUN=1;SAF=1745;SAP=6.90314;SAR=1825;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1841A>G|p.Asp614Gly|1841/3822|1841/3822|614/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1990A>G|||||1990|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2842A>G|||||2842|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3120A>G|||||3120|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3799A>G|||||3799|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3991A>G|||||3991|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4353A>G|||||4353|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4491A>G|||||4491|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4871A>G|||||4871|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1848A>G|||||1848|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3783A>G|||||3783|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2745A>G|||||2745|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1851A>G|||||1851|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:3572:2,3570:2:72:3570:124700:-10477.8,-1068.47,0
NC_045512.2	23472	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=35;CIGAR=1X;DP=2386;DPB=2386;DPRA=0;EPP=25.4075;EPPR=10.5077;GTI=0;LEN=1;MEANALT=2;MQM=53.7429;MQMR=48.1756;NS=1;NUMALT=1;ODDS=3053.41;PAIRED=1;PAIREDR=0.976556;PAO=0;PQA=0;PQR=0;PRO=0;QA=546;QR=77493;RO=2346;RPL=27;RPP=25.4075;RPPR=1331.44;RPR=8;RUN=1;SAF=35;SAP=79.0118;SAR=0;SRF=1114;SRP=15.8984;SRR=1232;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1910C>A|p.Ser637Tyr|1910/3822|1910/3822|637/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1921C>A|||||1921|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2773C>A|||||2773|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3051C>A|||||3051|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3730C>A|||||3730|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3922C>A|||||3922|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4284C>A|||||4284|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4422C>A|||||4422|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4802C>A|||||4802|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1917C>A|||||1917|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3852C>A|||||3852|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2814C>A|||||2814|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1920C>A|||||1920|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2386:2346,35:2346:77493:35:546:0,-668.526,-6266.09
NC_045512.2	23492	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=22;CIGAR=1X;DP=1868;DPB=1868;DPRA=0;EPP=42.4916;EPPR=19.2094;GTI=0;LEN=1;MEANALT=3;MQM=49.7273;MQMR=46.6534;NS=1;NUMALT=1;ODDS=2434.25;PAIRED=1;PAIREDR=0.973842;PAO=0;PQA=0;PQR=0;PRO=0;QA=327;QR=61631;RO=1835;RPL=21;RPP=42.4916;RPPR=2188.54;RPR=1;RUN=1;SAF=22;SAP=50.7827;SAR=0;SRF=857;SRP=20.3359;SRR=978;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.1930C>A|p.Gln644Lys|1930/3822|1930/3822|644/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1901C>A|||||1901|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2753C>A|||||2753|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-3031C>A|||||3031|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3710C>A|||||3710|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3902C>A|||||3902|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4264C>A|||||4264|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4402C>A|||||4402|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4782C>A|||||4782|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*1937C>A|||||1937|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3872C>A|||||3872|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2834C>A|||||2834|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*1940C>A|||||1940|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1868:1835,22:1835:61631:22:327:0,-529.793,-4862.4
NC_045512.2	23575	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=456;DPB=456;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=27.8333;MQMR=51.192;NS=1;NUMALT=1;ODDS=580.51;PAIRED=1;PAIREDR=0.991071;PAO=0;PQA=0;PQR=0;PRO=0;QA=208;QR=15391;RO=448;RPL=4;RPP=4.45795;RPPR=5.35627;RPR=2;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=229;SRP=3.495;SRR=219;TYPE=snp;ANN=T|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2013C>T|p.Cys671Cys|2013/3822|2013/3822|671/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1818C>T|||||1818|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2670C>T|||||2670|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2948C>T|||||2948|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3627C>T|||||3627|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3819C>T|||||3819|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4181C>T|||||4181|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4319C>T|||||4319|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4699C>T|||||4699|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2020C>T|||||2020|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3955C>T|||||3955|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2917C>T|||||2917|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2023C>T|||||2023|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:456:448,6:448:15391:6:208:0,-124.875,-1294.11
NC_045512.2	23604	.	C	G	15167.8	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=536;CIGAR=1X;DP=536;DPB=536;DPRA=0;EPP=3.0265;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.2929;MQMR=0;NS=1;NUMALT=1;ODDS=747.659;PAIRED=0.998134;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=18474;QR=0;RO=0;RPL=228;RPP=28.9383;RPPR=0;RPR=308;RUN=1;SAF=275;SAP=3.80435;SAR=261;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2042C>G|p.Pro681Arg|2042/3822|2042/3822|681/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1789C>G|||||1789|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2641C>G|||||2641|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2919C>G|||||2919|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3598C>G|||||3598|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3790C>G|||||3790|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4152C>G|||||4152|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4290C>G|||||4290|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4670C>G|||||4670|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2049C>G|||||2049|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*3984C>G|||||3984|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*2946C>G|||||2946|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2052C>G|||||2052|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	1/1:536:0,536:0:0:536:18474:-1523.85,-161.352,0
NC_045512.2	23746	.	A	G	1.18854E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1X;DP=618;DPB=618;DPRA=0;EPP=3.93042;EPPR=3.88433;GTI=0;LEN=1;MEANALT=1;MQM=52.9492;MQMR=52.1896;NS=1;NUMALT=1;ODDS=268.144;PAIRED=1;PAIREDR=0.989267;PAO=0;PQA=0;PQR=0;PRO=0;QA=2051;QR=19534;RO=559;RPL=32;RPP=3.93042;RPPR=5.84215;RPR=27;RUN=1;SAF=29;SAP=3.0471;SAR=30;SRF=268;SRP=5.06524;SRR=291;TYPE=snp;ANN=G|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2184A>G|p.Pro728Pro|2184/3822|2184/3822|728/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1647A>G|||||1647|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2499A>G|||||2499|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2777A>G|||||2777|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3456A>G|||||3456|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3648A>G|||||3648|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4010A>G|||||4010|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4148A>G|||||4148|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4528A>G|||||4528|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2191A>G|||||2191|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4126A>G|||||4126|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3088A>G|||||3088|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2194A>G|||||2194|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:618:559,59:559:19534:59:2051:0,-8.56006,-1510.11
NC_045512.2	23865	.	C	T	7.83587E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=325;DPB=325;DPRA=0;EPP=3.0103;EPPR=3.34385;GTI=0;LEN=1;MEANALT=1;MQM=49;MQMR=51.4671;NS=1;NUMALT=1;ODDS=391.092;PAIRED=1;PAIREDR=0.984326;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=11241;RO=319;RPL=0;RPP=16.0391;RPPR=3.56168;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=161;SRP=3.07156;SRR=158;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2303C>T|p.Thr768Ile|2303/3822|2303/3822|768/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1528C>T|||||1528|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2380C>T|||||2380|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2658C>T|||||2658|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3337C>T|||||3337|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3529C>T|||||3529|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3891C>T|||||3891|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4029C>T|||||4029|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4409C>T|||||4409|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2310C>T|||||2310|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4245C>T|||||4245|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3207C>T|||||3207|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2313C>T|||||2313|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:325:319,6:319:11241:6:204:0,-79.3917,-944.349
NC_045512.2	23887	.	CAAAAACACCCAAG	CAAAACACCCAAG	4.52052E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1M1D12M;DP=304;DPB=303.714;DPRA=0;EPP=3.0103;EPPR=4.05261;GTI=0;LEN=1;MEANALT=1;MQM=56.75;MQMR=52.8033;NS=1;NUMALT=1;ODDS=380.478;PAIRED=1;PAIREDR=0.963333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=10487;RO=300;RPL=4;RPP=11.6962;RPPR=3.12611;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=150;SRP=3.0103;SRR=150;TYPE=del;ANN=CAAAACACCCAAG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2330delA|p.Asn777fs|2330/3822|2330/3822|777/1273||,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1501delA|||||1501|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2353delA|||||2353|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2631delA|||||2631|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3310delA|||||3310|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3502delA|||||3502|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3864delA|||||3864|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-4002delA|||||4002|,CAAAACACCCAAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4382delA|||||4382|,CAAAACACCCAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2337delA|||||2337|,CAAAACACCCAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4272delA|||||4272|WARNING_TRANSCRIPT_NO_START_CODON,CAAAACACCCAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3234delA|||||3234|WARNING_TRANSCRIPT_NO_START_CODON,CAAAACACCCAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2340delA|||||2340|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:304:300,4:300:10487:4:144:0,-78.2128,-896.486
NC_045512.2	23910	.	C	T	1.37419E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=401;DPB=401;DPRA=0;EPP=3.0103;EPPR=3.14773;GTI=0;LEN=1;MEANALT=1;MQM=55.1667;MQMR=50.9089;NS=1;NUMALT=1;ODDS=489.483;PAIRED=1;PAIREDR=0.959494;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=13744;RO=395;RPL=2;RPP=4.45795;RPPR=11.3718;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=203;SRP=3.67549;SRR=192;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2348C>T|p.Ala783Val|2348/3822|2348/3822|783/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1483C>T|||||1483|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2335C>T|||||2335|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2613C>T|||||2613|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3292C>T|||||3292|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3484C>T|||||3484|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3846C>T|||||3846|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3984C>T|||||3984|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4364C>T|||||4364|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2355C>T|||||2355|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4290C>T|||||4290|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3252C>T|||||3252|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2358C>T|||||2358|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:401:395,6:395:13744:6:216:0,-100.971,-1131.25
NC_045512.2	23996	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=555;DPB=555;DPRA=0;EPP=3.0103;EPPR=3.58091;GTI=0;LEN=1;MEANALT=2;MQM=54.6667;MQMR=50.4818;NS=1;NUMALT=1;ODDS=702.743;PAIRED=1;PAIREDR=0.972628;PAO=0;PQA=0;PQR=0;PRO=0;QA=216;QR=19193;RO=548;RPL=0;RPP=16.0391;RPPR=7.06794;RPR=6;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=276;SRP=3.0737;SRR=272;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2434C>T|p.Pro812Ser|2434/3822|2434/3822|812/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1397C>T|||||1397|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2249C>T|||||2249|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2527C>T|||||2527|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3206C>T|||||3206|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3398C>T|||||3398|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3760C>T|||||3760|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3898C>T|||||3898|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4278C>T|||||4278|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2441C>T|||||2441|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4376C>T|||||4376|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3338C>T|||||3338|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2444C>T|||||2444|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:555:548,6:548:19193:6:216:0,-147.202,-1587.52
NC_045512.2	24110	.	A	C	9.9567E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=569;DPB=569;DPRA=0;EPP=3.9627;EPPR=3.62103;GTI=0;LEN=1;MEANALT=1;MQM=47.2807;MQMR=48.4238;NS=1;NUMALT=1;ODDS=274.15;PAIRED=1;PAIREDR=0.935547;PAO=0;PQA=0;PQR=0;PRO=0;QA=2023;QR=18082;RO=512;RPL=0;RPP=126.784;RPPR=3.02726;RPR=57;RUN=1;SAF=31;SAP=3.9627;SAR=26;SRF=253;SRP=3.16298;SRR=259;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2548A>C|p.Ile850Leu|2548/3822|2548/3822|850/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1283A>C|||||1283|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2135A>C|||||2135|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2413A>C|||||2413|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3092A>C|||||3092|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3284A>C|||||3284|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3646A>C|||||3646|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3784A>C|||||3784|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4164A>C|||||4164|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2555A>C|||||2555|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4490A>C|||||4490|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3452A>C|||||3452|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2558A>C|||||2558|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:569:512,57:512:18082:57:2023:0,-5.64707,-1298.89
NC_045512.2	24201	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=12;CIGAR=1X;DP=542;DPB=542;DPRA=0;EPP=3.73412;EPPR=3.21144;GTI=0;LEN=1;MEANALT=2;MQM=50.9167;MQMR=52.3214;NS=1;NUMALT=1;ODDS=625.015;PAIRED=1;PAIREDR=0.964083;PAO=0;PQA=0;PQR=0;PRO=0;QA=428;QR=18455;RO=529;RPL=11;RPP=21.1059;RPPR=31.2887;RPR=1;RUN=1;SAF=6;SAP=3.0103;SAR=6;SRF=266;SRP=3.04724;SRR=263;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2639G>A|p.Gly880Asp|2639/3822|2639/3822|880/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1192G>A|||||1192|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-2044G>A|||||2044|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2322G>A|||||2322|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-3001G>A|||||3001|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3193G>A|||||3193|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3555G>A|||||3555|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3693G>A|||||3693|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-4073G>A|||||4073|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2646G>A|||||2646|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4581G>A|||||4581|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3543G>A|||||3543|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2649G>A|||||2649|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:542:529,12:529:18455:12:428:0,-126.755,-1553.36
NC_045512.2	24320	.	CAAAAATTG	CAAAATTG	2687.09	.	AB=0.320298;ABP=153.634;AC=1;AF=0.5;AN=2;AO=172;CIGAR=1M1D7M;DP=537;DPB=519.222;DPRA=0;EPP=3.46479;EPPR=3.88374;GTI=0;LEN=1;MEANALT=3;MQM=49.6395;MQMR=53.9553;NS=1;NUMALT=1;ODDS=618.726;PAIRED=1;PAIREDR=0.997207;PAO=1;PQA=34.5;PQR=34.5;PRO=1;QA=5084;QR=12491;RO=358;RPL=99;RPP=11.5447;RPPR=3.22866;RPR=73;RUN=1;SAF=84;SAP=3.2123;SAR=88;SRF=175;SRP=3.3985;SRR=183;TYPE=del;ANN=CAAAATTG|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2763delA|p.Lys921fs|2763/3822|2763/3822|921/1273||,CAAAATTG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1068delA|||||1068|,CAAAATTG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1920delA|||||1920|,CAAAATTG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2198delA|||||2198|,CAAAATTG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2877delA|||||2877|,CAAAATTG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3069delA|||||3069|,CAAAATTG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3431delA|||||3431|,CAAAATTG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3569delA|||||3569|,CAAAATTG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3949delA|||||3949|,CAAAATTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2770delA|||||2770|,CAAAATTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4705delA|||||4705|WARNING_TRANSCRIPT_NO_START_CODON,CAAAATTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3667delA|||||3667|WARNING_TRANSCRIPT_NO_START_CODON,CAAAATTG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2773delA|||||2773|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(S|GU280_gp02|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:537:358,172:358:12491:172:5084:-291.188,0,-941.405
NC_045512.2	24329	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=6;CIGAR=1X;DP=563;DPB=563;DPRA=0;EPP=3.0103;EPPR=3.04539;GTI=0;LEN=1;MEANALT=1;MQM=54.3333;MQMR=52.1598;NS=1;NUMALT=1;ODDS=713.029;PAIRED=1;PAIREDR=0.994614;PAO=0;PQA=0;PQR=0;PRO=0;QA=211;QR=19533;RO=557;RPL=2;RPP=4.45795;RPPR=8.93994;RPR=4;RUN=1;SAF=3;SAP=3.0103;SAR=3;SRF=271;SRP=3.88747;SRR=286;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2767A>G|p.Ile923Val|2767/3822|2767/3822|923/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-1064A>G|||||1064|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1916A>G|||||1916|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2194A>G|||||2194|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2873A>G|||||2873|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-3065A>G|||||3065|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3427A>G|||||3427|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3565A>G|||||3565|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3945A>G|||||3945|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2774A>G|||||2774|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4709A>G|||||4709|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3671A>G|||||3671|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2777A>G|||||2777|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:563:557,6:557:19533:6:211:0,-150.179,-1654.98
NC_045512.2	24410	.	G	A	7223.05	.	AB=0.387777;ABP=106.822;AC=1;AF=0.5;AN=2;AO=368;CIGAR=1X;DP=949;DPB=949;DPRA=0;EPP=3.86001;EPPR=6.84407;GTI=0;LEN=1;MEANALT=2;MQM=45.2799;MQMR=49.4586;NS=1;NUMALT=1;ODDS=1663.17;PAIRED=0.98913;PAIREDR=0.993103;PAO=0;PQA=0;PQR=0;PRO=0;QA=13128;QR=20569;RO=580;RPL=255;RPP=121.993;RPPR=1202.4;RPR=113;RUN=1;SAF=177;SAP=4.16685;SAR=191;SRF=307;SRP=7.33827;SRR=273;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2848G>A|p.Asp950Asn|2848/3822|2848/3822|950/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-983G>A|||||983|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1835G>A|||||1835|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2113G>A|||||2113|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2792G>A|||||2792|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2984G>A|||||2984|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3346G>A|||||3346|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3484G>A|||||3484|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3864G>A|||||3864|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2855G>A|||||2855|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4790G>A|||||4790|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3752G>A|||||3752|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2858G>A|||||2858|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:949:580,368:580:20569:368:13128:-752.784,0,-1403.38
NC_045512.2	24506	.	T	G	13690.0	.	AB=0.316547;ABP=653.14;AC=1;AF=0.5;AN=2;AO=704;CIGAR=1X;DP=2224;DPB=2224;DPRA=0;EPP=3.61486;EPPR=3.76653;GTI=0;LEN=1;MEANALT=2;MQM=51.4545;MQMR=52.4332;NS=1;NUMALT=1;ODDS=3152.23;PAIRED=0.992898;PAIREDR=0.99605;PAO=0;PQA=0;PQR=0;PRO=0;QA=24742;QR=53799;RO=1519;RPL=390;RPP=20.8262;RPPR=19.9947;RPR=314;RUN=1;SAF=361;SAP=4.00967;SAR=343;SRF=776;SRP=4.56707;SRR=743;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.2944T>G|p.Ser982Ala|2944/3822|2944/3822|982/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-887T>G|||||887|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1739T>G|||||1739|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-2017T>G|||||2017|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2696T>G|||||2696|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2888T>G|||||2888|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3250T>G|||||3250|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3388T>G|||||3388|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3768T>G|||||3768|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*2951T>G|||||2951|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725309.1|protein_coding||c.*4886T>G|||||4886|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3848T>G|||||3848|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*2954T>G|||||2954|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2224:1519,704:1519:53799:704:24742:-1445.67,0,-3985.74
NC_045512.2	24626	.	G	A	1.2247E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=45;CIGAR=1X;DP=2469;DPB=2469;DPRA=0;EPP=3.05855;EPPR=4.04844;GTI=0;LEN=1;MEANALT=3;MQM=46.8667;MQMR=52.6319;NS=1;NUMALT=1;ODDS=2917.41;PAIRED=1;PAIREDR=0.995451;PAO=0;PQA=0;PQR=0;PRO=0;QA=1578;QR=84277;RO=2418;RPL=27;RPP=6.91895;RPPR=3.52757;RPR=18;RUN=1;SAF=23;SAP=3.05855;SAR=22;SRF=1205;SRP=3.06777;SRR=1213;TYPE=snp;ANN=A|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3064G>A|p.Ala1022Thr|3064/3822|3064/3822|1022/1273||,A|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-767G>A|||||767|,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1619G>A|||||1619|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1897G>A|||||1897|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2576G>A|||||2576|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2768G>A|||||2768|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-3130G>A|||||3130|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3268G>A|||||3268|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3648G>A|||||3648|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4932G>A|||||4932|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3071G>A|||||3071|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*3968G>A|||||3968|WARNING_TRANSCRIPT_NO_START_CODON,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3074G>A|||||3074|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2469:2418,45:2418:84277:45:1578:0,-616.766,-7159.4
NC_045512.2	24794	.	G	C	4292.7	.	AB=0.176533;ABP=3441.96;AC=1;AF=0.5;AN=2;AO=668;CIGAR=1X;DP=3784;DPB=3784;DPRA=0;EPP=3.4784;EPPR=4.48774;GTI=0;LEN=1;MEANALT=3;MQM=49.018;MQMR=52.3277;NS=1;NUMALT=1;ODDS=988.432;PAIRED=1;PAIREDR=0.994534;PAO=0;PQA=0;PQR=0;PRO=0;QA=23418;QR=109332;RO=3110;RPL=267;RPP=61.38;RPPR=173.402;RPR=401;RUN=1;SAF=341;SAP=3.64744;SAR=327;SRF=1584;SRP=5.35912;SRR=1526;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3232G>C|p.Ala1078Pro|3232/3822|3232/3822|1078/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-599G>C|||||599|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1451G>C|||||1451|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1729G>C|||||1729|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2408G>C|||||2408|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2600G>C|||||2600|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2962G>C|||||2962|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-3100G>C|||||3100|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3480G>C|||||3480|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4764G>C|||||4764|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3239G>C|||||3239|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4136G>C|||||4136|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3242G>C|||||3242|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3784:3110,668:3110:109332:668:23418:-815.381,0,-8328.87
NC_045512.2	24914	.	G	C	16119.5	.	AB=0.236327;ABP=2962;AC=1;AF=0.5;AN=2;AO=1158;CIGAR=1X;DP=4900;DPB=4900;DPRA=0;EPP=3.19782;EPPR=3.53313;GTI=0;LEN=1;MEANALT=2;MQM=50.032;MQMR=52.79;NS=1;NUMALT=1;ODDS=3711.66;PAIRED=0.996546;PAIREDR=0.991974;PAO=0;PQA=0;PQR=0;PRO=0;QA=40628;QR=131352;RO=3738;RPL=527;RPP=23.2924;RPPR=15.0562;RPR=631;RUN=1;SAF=591;SAP=4.09041;SAR=567;SRF=1865;SRP=3.04748;SRR=1873;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3352G>C|p.Asp1118His|3352/3822|3352/3822|1118/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-479G>C|||||479|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1331G>C|||||1331|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1609G>C|||||1609|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2288G>C|||||2288|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2480G>C|||||2480|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2842G>C|||||2842|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2980G>C|||||2980|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3360G>C|||||3360|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4644G>C|||||4644|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3359G>C|||||3359|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4256G>C|||||4256|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3362G>C|||||3362|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4900:3738,1158:3738:131352:1158:40628:-1933.55,0,-9894.85
NC_045512.2	24952	.	A	G	9.54689E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=70;CIGAR=1X;DP=4842;DPB=4842;DPRA=0;EPP=3.0103;EPPR=10.9423;GTI=0;LEN=1;MEANALT=2;MQM=51.7714;MQMR=52.1543;NS=1;NUMALT=1;ODDS=5869.66;PAIRED=1;PAIREDR=0.991824;PAO=0;PQA=0;PQR=0;PRO=0;QA=2463;QR=167916;RO=4770;RPL=37;RPP=3.50664;RPPR=21.9554;RPR=33;RUN=1;SAF=36;SAP=3.13438;SAR=34;SRF=2328;SRP=8.92654;SRR=2442;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3390A>G|p.Ile1130Met|3390/3822|3390/3822|1130/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-441A>G|||||441|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1293A>G|||||1293|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1571A>G|||||1571|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2250A>G|||||2250|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2442A>G|||||2442|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2804A>G|||||2804|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2942A>G|||||2942|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3322A>G|||||3322|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4606A>G|||||4606|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3397A>G|||||3397|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4294A>G|||||4294|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3400A>G|||||3400|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4842:4770,70:4770:167916:70:2463:0,-1244.69,-14195.3
NC_045512.2	25047	.	C	T	6.36456E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=333;CIGAR=1X;DP=4648;DPB=4648;DPRA=0;EPP=3.79933;EPPR=13.3153;GTI=0;LEN=1;MEANALT=2;MQM=46.3183;MQMR=51.3063;NS=1;NUMALT=1;ODDS=3139.76;PAIRED=0.993994;PAIREDR=0.986076;PAO=0;PQA=0;PQR=0;PRO=0;QA=11708;QR=149413;RO=4309;RPL=109;RPP=89.2497;RPPR=163.88;RPR=224;RUN=1;SAF=173;SAP=4.11234;SAR=160;SRF=2131;SRP=4.1235;SRR=2178;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3485C>T|p.Pro1162Leu|3485/3822|3485/3822|1162/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-346C>T|||||346|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1198C>T|||||1198|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1476C>T|||||1476|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-2155C>T|||||2155|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2347C>T|||||2347|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2709C>T|||||2709|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2847C>T|||||2847|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3227C>T|||||3227|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4511C>T|||||4511|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3492C>T|||||3492|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4389C>T|||||4389|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3495C>T|||||3495|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4648:4309,333:4309:149413:333:11708:0,-469.855,-11790.8
NC_045512.2	25243	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=69;CIGAR=1X;DP=3225;DPB=3225;DPRA=0;EPP=3.04177;EPPR=3.63033;GTI=0;LEN=1;MEANALT=2;MQM=52.7681;MQMR=52.0352;NS=1;NUMALT=1;ODDS=3678.35;PAIRED=1;PAIREDR=0.993655;PAO=0;PQA=0;PQR=0;PRO=0;QA=2355;QR=108908;RO=3152;RPL=40;RPP=6.81824;RPPR=95.2951;RPR=29;RUN=1;SAF=34;SAP=3.04177;SAR=35;SRF=1538;SRP=6.9895;SRR=1614;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3681A>G|p.Ile1227Met|3681/3822|3681/3822|1227/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-150A>G|||||150|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1002A>G|||||1002|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1280A>G|||||1280|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1959A>G|||||1959|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2151A>G|||||2151|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2513A>G|||||2513|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2651A>G|||||2651|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3031A>G|||||3031|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4315A>G|||||4315|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3688A>G|||||3688|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4585A>G|||||4585|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3691A>G|||||3691|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3225:3152,69:3152:108908:69:2355:0,-765.93,-9146.09
NC_045512.2	25244	.	G	T	8.47644E-13	.	AB=0.135368;ABP=3748.16;AC=1;AF=0.5;AN=2;AO=439;CIGAR=1X;DP=3243;DPB=3243;DPRA=0;EPP=4.12324;EPPR=4.37735;GTI=0;LEN=1;MEANALT=3;MQM=48.303;MQMR=52.5899;NS=1;NUMALT=1;ODDS=418.437;PAIRED=0.995444;PAIREDR=0.99429;PAO=0;PQA=0;PQR=0;PRO=0;QA=15155;QR=97802;RO=2802;RPL=270;RPP=53.4686;RPPR=74.6301;RPR=169;RUN=1;SAF=216;SAP=3.25267;SAR=223;SRF=1369;SRP=6.18459;SRR=1433;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3682G>T|p.Val1228Leu|3682/3822|3682/3822|1228/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-149G>T|||||149|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-1001G>T|||||1001|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1279G>T|||||1279|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1958G>T|||||1958|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2150G>T|||||2150|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2512G>T|||||2512|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2650G>T|||||2650|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-3030G>T|||||3030|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4314G>T|||||4314|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3689G>T|||||3689|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4586G>T|||||4586|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3692G>T|||||3692|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3243:2802,439:2802:97802:439:15155:-248.813,0,-7498.01
NC_045512.2	25277	.	A	T	2.24204E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=49;CIGAR=1X;DP=2415;DPB=2415;DPRA=0;EPP=100.904;EPPR=7.6624;GTI=0;LEN=1;MEANALT=3;MQM=51.7551;MQMR=50.6511;NS=1;NUMALT=1;ODDS=3038.7;PAIRED=0.979592;PAIREDR=0.9932;PAO=0;PQA=0;PQR=0;PRO=0;QA=748;QR=81205;RO=2353;RPL=1;RPP=100.904;RPPR=938.828;RPR=48;RUN=1;SAF=0;SAP=109.412;SAR=49;SRF=1196;SRP=4.41396;SRR=1157;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3715A>T|p.Ser1239Cys|3715/3822|3715/3822|1239/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-116A>T|||||116|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-968A>T|||||968|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1246A>T|||||1246|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1925A>T|||||1925|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2117A>T|||||2117|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2479A>T|||||2479|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2617A>T|||||2617|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2997A>T|||||2997|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4281A>T|||||4281|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3722A>T|||||3722|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4619A>T|||||4619|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3725A>T|||||3725|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2415:2353,49:2353:81205:49:748:0,-656.393,-6775.09
NC_045512.2	25286	.	A	T	6.2686E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=2593;DPB=2593;DPRA=0;EPP=163.699;EPPR=57.3406;GTI=0;LEN=1;MEANALT=2;MQM=50.9459;MQMR=49.8839;NS=1;NUMALT=1;ODDS=3162.15;PAIRED=0.959459;PAIREDR=0.988391;PAO=0;PQA=0;PQR=0;PRO=0;QA=1109;QR=84675;RO=2498;RPL=0;RPP=163.699;RPPR=507.755;RPR=74;RUN=1;SAF=0;SAP=163.699;SAR=74;SRF=1342;SRP=33.0841;SRR=1156;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3724A>T|p.Ser1242Cys|3724/3822|3724/3822|1242/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-107A>T|||||107|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-959A>T|||||959|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1237A>T|||||1237|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1916A>T|||||1916|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2108A>T|||||2108|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2470A>T|||||2470|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2608A>T|||||2608|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2988A>T|||||2988|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4272A>T|||||4272|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3731A>T|||||3731|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4628A>T|||||4628|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3734A>T|||||3734|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2593:2498,74:2498:84675:74:1109:0,-674.605,-6923.8
NC_045512.2	25296	.	A	C,T	1.83222E-13	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=141,54;CIGAR=1X,1X;DP=2571;DPB=2571;DPRA=0,0;EPP=119.577,88.0998;EPPR=157.455;GTI=0;LEN=1,1;MEANALT=3,3;MQM=50.9149,51.6111;MQMR=49.8522;NS=1;NUMALT=2;ODDS=2652.62;PAIRED=0.957447,0.981481;PAIREDR=0.988632;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=2213,924;QR=80940;RO=2375;RPL=28,4;RPP=114.279,88.0998;RPPR=367.051;RPR=113,50;RUN=1,1;SAF=1,0;SAP=300.564,120.27;SAR=140,54;SRF=1364;SRP=116.941;SRR=1011;TYPE=snp,snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3734A>C|p.Lys1245Thr|3734/3822|3734/3822|1245/1273||,T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3734A>T|p.Lys1245Met|3734/3822|3734/3822|1245/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-97A>C|||||97|,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-97A>T|||||97|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-949A>C|||||949|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-949A>T|||||949|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1227A>C|||||1227|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1227A>T|||||1227|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1906A>C|||||1906|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1906A>T|||||1906|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2098A>C|||||2098|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2098A>T|||||2098|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2460A>C|||||2460|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2460A>T|||||2460|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2598A>C|||||2598|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2598A>T|||||2598|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2978A>C|||||2978|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2978A>T|||||2978|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4262A>C|||||4262|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4262A>T|||||4262|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3741A>C|||||3741|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3741A>T|||||3741|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4638A>C|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4638A>T|||||4638|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3744A>C|||||3744|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3744A>T|||||3744|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2571:2375,141,54:2375:80940:141,54:2213,924:0,-560.207,-6463.48,-648.053,-6439.04,-6577.52
NC_045512.2	25297	.	GGGC	GGGG	1.29702E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=63;CIGAR=3M1X;DP=2484;DPB=2543.75;DPRA=0;EPP=114.996;EPPR=62.0599;GTI=0;LEN=1;MEANALT=9;MQM=50.7937;MQMR=49.9929;NS=1;NUMALT=1;ODDS=2993.64;PAIRED=0.952381;PAIREDR=0.987137;PAO=66;PQA=2152;PQR=2152;PRO=66;QA=1266;QR=82158;RO=2410;RPL=3;RPP=114.996;RPPR=193.667;RPR=60;RUN=1;SAF=0;SAP=139.813;SAR=63;SRF=1322;SRP=52.3469;SRR=1088;TYPE=snp;ANN=GGGG|synonymous_variant|LOW|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3738C>G|p.Gly1246Gly|3738/3822|3738/3822|1246/1273||,GGGG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-93C>G|||||93|,GGGG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-945C>G|||||945|,GGGG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1223C>G|||||1223|,GGGG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1902C>G|||||1902|,GGGG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2094C>G|||||2094|,GGGG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2456C>G|||||2456|,GGGG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2594C>G|||||2594|,GGGG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2974C>G|||||2974|,GGGG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4258C>G|||||4258|,GGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3745C>G|||||3745|,GGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4642C>G|||||4642|WARNING_TRANSCRIPT_NO_START_CODON,GGGG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3748C>G|||||3748|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2484:2410,63:2410:82158:63:1266:0,-632.107,-6695.99
NC_045512.2	25308	.	C	G,T	1.02822E-13	.	AB=0,0;ABP=0,0;AC=0,0;AF=0,0;AN=2;AO=27,37;CIGAR=1X,1X;DP=2591;DPB=2591;DPRA=0,0;EPP=38.4777,74.9036;EPPR=105.533;GTI=0;LEN=1,1;MEANALT=3,3;MQM=47.9259,50.0541;MQMR=50.213;NS=1;NUMALT=2;ODDS=3317.27;PAIRED=0.888889,0.972973;PAIREDR=0.981357;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=392,554;QR=79400;RO=2521;RPL=4,1;RPP=32.0437,74.9036;RPPR=90.6625;RPR=23,36;RUN=1,1;SAF=1,0;SAP=53.2759,83.3548;SAR=26,37;SRF=1425;SRP=96.2441;SRR=1096;TYPE=snp,snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3746C>G|p.Ser1249Cys|3746/3822|3746/3822|1249/1273||,T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3746C>T|p.Ser1249Phe|3746/3822|3746/3822|1249/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-85C>G|||||85|,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-85C>T|||||85|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-937C>G|||||937|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-937C>T|||||937|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1215C>G|||||1215|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1215C>T|||||1215|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1894C>G|||||1894|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1894C>T|||||1894|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2086C>G|||||2086|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2086C>T|||||2086|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2448C>G|||||2448|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2448C>T|||||2448|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2586C>G|||||2586|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2586C>T|||||2586|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2966C>G|||||2966|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2966C>T|||||2966|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4250C>G|||||4250|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4250C>T|||||4250|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3753C>G|||||3753|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3753C>T|||||3753|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4650C>G|||||4650|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4650C>T|||||4650|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3756C>G|||||3756|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3756C>T|||||3756|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2591:2521,27,37:2521:79400:27,37:392,554:0,-732.46,-6524.72,-721.199,-6495.15,-6510.45
NC_045512.2	25312	.	T	G	1.87444E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=29;CIGAR=1X;DP=2594;DPB=2594;DPRA=0;EPP=3.68421;EPPR=76.7412;GTI=0;LEN=1;MEANALT=3;MQM=46.4483;MQMR=50.2856;NS=1;NUMALT=1;ODDS=3381;PAIRED=0.896552;PAIREDR=0.980101;PAO=0;PQA=0;PQR=0;PRO=0;QA=439;QR=80737;RO=2563;RPL=13;RPP=3.68421;RPPR=17.1092;RPR=16;RUN=1;SAF=0;SAP=65.983;SAR=29;SRF=1423;SRP=70.8648;SRR=1140;TYPE=snp;ANN=G|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3750T>G|p.Cys1250Trp|3750/3822|3750/3822|1250/1273||,G|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-81T>G|||||81|,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-933T>G|||||933|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1211T>G|||||1211|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1890T>G|||||1890|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2082T>G|||||2082|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2444T>G|||||2444|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2582T>G|||||2582|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2962T>G|||||2962|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4246T>G|||||4246|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3757T>G|||||3757|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4654T>G|||||4654|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3760T>G|||||3760|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2594:2563,29:2563:80737:29:439:0,-743.535,-6638.88
NC_045512.2	25314	.	G	T	5.47261E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=98;CIGAR=1X;DP=2511;DPB=2511;DPRA=0;EPP=124.347;EPPR=150.808;GTI=0;LEN=1;MEANALT=2;MQM=49.5816;MQMR=50.4178;NS=1;NUMALT=1;ODDS=2901.26;PAIRED=0.938776;PAIREDR=0.982068;PAO=0;PQA=0;PQR=0;PRO=0;QA=1409;QR=74838;RO=2398;RPL=12;RPP=124.347;RPPR=10.6747;RPR=86;RUN=1;SAF=0;SAP=215.815;SAR=98;SRF=1406;SRP=158.215;SRR=992;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3752G>T|p.Gly1251Val|3752/3822|3752/3822|1251/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-79G>T|||||79|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-931G>T|||||931|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1209G>T|||||1209|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1888G>T|||||1888|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2080G>T|||||2080|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2442G>T|||||2442|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2580G>T|||||2580|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2960G>T|||||2960|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4244G>T|||||4244|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3759G>T|||||3759|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4656G>T|||||4656|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3762G>T|||||3762|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2511:2398,98:2398:74838:98:1409:0,-626.065,-6055.73
NC_045512.2	25316	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=38;CIGAR=1X;DP=2470;DPB=2470;DPRA=0;EPP=17.6392;EPPR=126.463;GTI=0;LEN=1;MEANALT=3;MQM=48.9737;MQMR=50.4211;NS=1;NUMALT=1;ODDS=3112.87;PAIRED=0.973684;PAIREDR=0.979236;PAO=0;PQA=0;PQR=0;PRO=0;QA=605;QR=74347;RO=2408;RPL=10;RPP=21.525;RPPR=4.75613;RPR=28;RUN=1;SAF=1;SAP=77.0689;SAR=37;SRF=1393;SRP=131.859;SRR=1015;TYPE=snp;ANN=C|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3754T>C|p.Ser1252Pro|3754/3822|3754/3822|1252/1273||,C|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-77T>C|||||77|,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-929T>C|||||929|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1207T>C|||||1207|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1886T>C|||||1886|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2078T>C|||||2078|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2440T>C|||||2440|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2578T>C|||||2578|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2958T>C|||||2958|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4242T>C|||||4242|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3761T>C|||||3761|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4658T>C|||||4658|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3764T>C|||||3764|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2470:2408,38:2408:74347:38:605:0,-682.516,-6085.67
NC_045512.2	25323	.	GCAAA	GAAAT,CAAAA,GAAAA	0.0	.	AB=0,0,0;ABP=0,0,0;AC=0,0,0;AF=0,0,0;AN=2;AO=71,67,284;CIGAR=1M1X2M1X,2X3M,1M1X3M;DP=2463;DPB=2473.6;DPRA=0,0,0;EPP=76.4428,38.3048,208.658;EPPR=686.769;GTI=0;LEN=5,2,1;MEANALT=17,17,17;MQM=48.8873,49.7164,50.9155;MQMR=51.4338;NS=1;NUMALT=3;ODDS=1480.75;PAIRED=0.901408,0.955224,0.985915;PAIREDR=0.977006;PAO=9,10,10;PQA=126,247,247;PQR=247;PRO=10;QA=1663,1100,5254;QR=66729;RO=1957;RPL=11,17,60;RPP=76.4428,38.3048,208.658;RPPR=21.475;RPR=60,50,224;RUN=1,1,1;SAF=0,0,0;SAP=157.185,148.499,619.708;SAR=71,67,284;SRF=1463;SRP=1044.87;SRR=494;TYPE=complex,mnp,snp;ANN=GAAAA|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3762C>A|p.Cys1254*|3762/3822|3762/3822|1254/1273||,GAAAT|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3762_3765delCAAAinsAAAT|p.CysLys1254*|3762/3822|3762/3822|1254/1273||,CAAAA|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3761_3762delGCinsCA|p.Cys1254Ser|3761/3822|3761/3822|1254/1273||,CAAAA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-70_-69delGCinsCA|||||70|,GAAAA|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-69C>A|||||69|,GAAAT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-69_-66delCAAAinsAAAT|||||69|,CAAAA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-922_-921delGCinsCA|||||922|,GAAAA|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-921C>A|||||921|,GAAAT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-921_-918delCAAAinsAAAT|||||921|,CAAAA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1200_-1199delGCinsCA|||||1200|,GAAAA|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1199C>A|||||1199|,GAAAT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1199_-1196delCAAAinsAAAT|||||1199|,CAAAA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1879_-1878delGCinsCA|||||1879|,GAAAA|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1878C>A|||||1878|,GAAAT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1878_-1875delCAAAinsAAAT|||||1878|,CAAAA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2071_-2070delGCinsCA|||||2071|,GAAAA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2070C>A|||||2070|,GAAAT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2070_-2067delCAAAinsAAAT|||||2070|,CAAAA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2433_-2432delGCinsCA|||||2433|,GAAAA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2432C>A|||||2432|,GAAAT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2432_-2429delCAAAinsAAAT|||||2432|,CAAAA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2571_-2570delGCinsCA|||||2571|,GAAAA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2570C>A|||||2570|,GAAAT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2570_-2567delCAAAinsAAAT|||||2570|,CAAAA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2951_-2950delGCinsCA|||||2951|,GAAAA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2950C>A|||||2950|,GAAAT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2950_-2947delCAAAinsAAAT|||||2950|,CAAAA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4235_-4234delGCinsCA|||||4235|,GAAAA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4234C>A|||||4234|,GAAAT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4234_-4231delCAAAinsAAAT|||||4234|,CAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3768_*3769delGCinsCA|||||3768|,GAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3769C>A|||||3769|,GAAAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3769_*3772delCAAAinsAAAT|||||3769|,CAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4665_*4666delGCinsCA|||||4665|WARNING_TRANSCRIPT_NO_START_CODON,GAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4666C>A|||||4666|WARNING_TRANSCRIPT_NO_START_CODON,GAAAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4666_*4669delCAAAinsAAAT|||||4666|WARNING_TRANSCRIPT_NO_START_CODON,CAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3771_*3772delGCinsCA|||||3771|WARNING_TRANSCRIPT_NO_START_CODON,GAAAA|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3772C>A|||||3772|WARNING_TRANSCRIPT_NO_START_CODON,GAAAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3772_*3775delCAAAinsAAAT|||||3772|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2463:1957,71,67,284:1957:66729:71,67,284:1663,1100,5254:0,-464.981,-5396.57,-511.087,-5339.92,-5443.88,-203.076,-5031.91,-5078.01,-5070.55
NC_045512.2	25331	.	G	T	1.83222E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=167;CIGAR=1X;DP=2694;DPB=2694;DPRA=0;EPP=135.652;EPPR=242.371;GTI=0;LEN=1;MEANALT=2;MQM=49.7964;MQMR=51.6339;NS=1;NUMALT=1;ODDS=2682.43;PAIRED=0.946108;PAIREDR=0.978884;PAO=0;PQA=0;PQR=0;PRO=0;QA=2950;QR=74828;RO=2510;RPL=33;RPP=135.652;RPPR=260.919;RPR=134;RUN=1;SAF=0;SAP=365.646;SAR=167;SRF=1594;SRP=400.696;SRR=916;TYPE=snp;ANN=T|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3769G>T|p.Asp1257Tyr|3769/3822|3769/3822|1257/1273||,T|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-62G>T|||||62|,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-914G>T|||||914|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1192G>T|||||1192|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1871G>T|||||1871|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2063G>T|||||2063|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2425G>T|||||2425|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2563G>T|||||2563|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2943G>T|||||2943|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4227G>T|||||4227|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3776G>T|||||3776|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4673G>T|||||4673|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3779G>T|||||3779|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2694:2510,167:2510:74828:167:2950:0,-546.112,-6035.79
NC_045512.2	25334	.	GAAG	CACG,CACC,GACC,CAAG,TAAG,GACG,GAAC	3.16299E-13	.	AB=0,0,0,0,0,0,0;ABP=0,0,0,0,0,0,0;AC=0,0,0,0,0,0,0;AF=0,0,0,0,0,0,0;AN=2;AO=70,48,48,67,57,133,35;CIGAR=1X1M1X1M,1X1M2X,2M2X,1X3M,1X3M,2M1X1M,3M1X;DP=2461;DPB=2518;DPRA=0,0,0,0,0,0,0;EPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;EPPR=603.572;GTI=0;LEN=4,4,2,1,1,1,1;MEANALT=17,17,17,17,17,17,17;MQM=49.1143,49.9583,46.0833,52.3134,50.9825,51.203,49.3143;MQMR=53.4979;NS=1;NUMALT=7;ODDS=2128.71;PAIRED=0.971429,0.958333,0.979167,1,0.982456,0.977444,0.971429;PAIREDR=0.975873;PAO=0,8.33333,41.5833,0,0,33.25,44.5833;PQA=0,188.333,1318.58,0,0,1130.25,1409.58;PQR=1221.25;PRO=36.25;QA=1249,803,708,1036,910,1875,507;QR=63002;RO=1948;RPL=14,16,14,16,11,41,6;RPP=57.7314,14.5915,21.1059,42.7126,49.6779,45.4765,35.8306;RPPR=494.485;RPR=56,32,34,51,46,92,29;RUN=1,1,1,1,1,1,1;SAF=0,0,0,0,0,0,0;SAP=155.013,107.241,107.241,148.499,126.784,291.816,79.0118;SAR=70,48,48,67,57,133,35;SRF=1469;SRP=1095.55;SRR=479;TYPE=complex,complex,mnp,snp,snp,snp,snp;ANN=TAAG|stop_gained|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772G>T|p.Glu1258*|3772/3822|3772/3822|1258/1273||,CAAG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772G>C|p.Glu1258Gln|3772/3822|3772/3822|1258/1273||,GACG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3774A>C|p.Glu1258Asp|3774/3822|3774/3822|1258/1273||,GAAC|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3775G>C|p.Asp1259His|3775/3822|3775/3822|1259/1273||,CACG|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772_3774delGAAinsCAC|p.Glu1258His|3772/3822|3772/3822|1258/1273||,CACC|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3772_3775delGAAGinsCACC|p.GluAsp1258HisHis|3772/3822|3772/3822|1258/1273||,GACC|missense_variant|MODERATE|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3774_3775delAGinsCC|p.GluAsp1258AspHis|3774/3822|3774/3822|1258/1273||,CAAG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-59G>C|||||59|,TAAG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-59G>T|||||59|,CACG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-59_-57delGAAinsCAC|||||59|,CACC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-59_-56delGAAGinsCACC|||||59|,GACG|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-57A>C|||||57|,GACC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-57_-56delAGinsCC|||||57|,GAAC|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-56G>C|||||56|,CAAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-911G>C|||||911|,TAAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-911G>T|||||911|,CACG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-911_-909delGAAinsCAC|||||911|,CACC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-911_-908delGAAGinsCACC|||||911|,GACG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-909A>C|||||909|,GACC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-909_-908delAGinsCC|||||909|,GAAC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-908G>C|||||908|,CAAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1189G>C|||||1189|,TAAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1189G>T|||||1189|,CACG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1189_-1187delGAAinsCAC|||||1189|,CACC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1189_-1186delGAAGinsCACC|||||1189|,GACG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1187A>C|||||1187|,GACC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1187_-1186delAGinsCC|||||1187|,GAAC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1186G>C|||||1186|,CAAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1868G>C|||||1868|,TAAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1868G>T|||||1868|,CACG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1868_-1866delGAAinsCAC|||||1868|,CACC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1868_-1865delGAAGinsCACC|||||1868|,GACG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1866A>C|||||1866|,GACC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1866_-1865delAGinsCC|||||1866|,GAAC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1865G>C|||||1865|,CAAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2060G>C|||||2060|,TAAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2060G>T|||||2060|,CACG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2060_-2058delGAAinsCAC|||||2060|,CACC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2060_-2057delGAAGinsCACC|||||2060|,GACG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2058A>C|||||2058|,GACC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2058_-2057delAGinsCC|||||2058|,GAAC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2057G>C|||||2057|,CAAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2422G>C|||||2422|,TAAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2422G>T|||||2422|,CACG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2422_-2420delGAAinsCAC|||||2422|,CACC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2422_-2419delGAAGinsCACC|||||2422|,GACG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2420A>C|||||2420|,GACC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2420_-2419delAGinsCC|||||2420|,GAAC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2419G>C|||||2419|,CAAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2560G>C|||||2560|,TAAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2560G>T|||||2560|,CACG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2560_-2558delGAAinsCAC|||||2560|,CACC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2560_-2557delGAAGinsCACC|||||2560|,GACG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2558A>C|||||2558|,GACC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2558_-2557delAGinsCC|||||2558|,GAAC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2557G>C|||||2557|,CAAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2940G>C|||||2940|,TAAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2940G>T|||||2940|,CACG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2940_-2938delGAAinsCAC|||||2940|,CACC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2940_-2937delGAAGinsCACC|||||2940|,GACG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2938A>C|||||2938|,GACC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2938_-2937delAGinsCC|||||2938|,GAAC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2937G>C|||||2937|,CAAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4224G>C|||||4224|,TAAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4224G>T|||||4224|,CACG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4224_-4222delGAAinsCAC|||||4224|,CACC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4224_-4221delGAAGinsCACC|||||4224|,GACG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4222A>C|||||4222|,GACC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4222_-4221delAGinsCC|||||4222|,GAAC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4221G>C|||||4221|,CAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3779G>C|||||3779|,TAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3779G>T|||||3779|,CACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3779_*3781delGAAinsCAC|||||3779|,CACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3779_*3782delGAAGinsCACC|||||3779|,GACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3781A>C|||||3781|,GACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3781_*3782delAGinsCC|||||3781|,GAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3782G>C|||||3782|,CAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4676G>C|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,TAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4676G>T|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,CACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4676_*4678delGAAinsCAC|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,CACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4676_*4679delGAAGinsCACC|||||4676|WARNING_TRANSCRIPT_NO_START_CODON,GACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4678A>C|||||4678|WARNING_TRANSCRIPT_NO_START_CODON,GACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4678_*4679delAGinsCC|||||4678|WARNING_TRANSCRIPT_NO_START_CODON,GAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4679G>C|||||4679|WARNING_TRANSCRIPT_NO_START_CODON,CAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3782G>C|||||3782|WARNING_TRANSCRIPT_NO_START_CODON,TAAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3782G>T|||||3782|WARNING_TRANSCRIPT_NO_START_CODON,CACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3782_*3784delGAAinsCAC|||||3782|WARNING_TRANSCRIPT_NO_START_CODON,CACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3782_*3785delGAAGinsCACC|||||3782|WARNING_TRANSCRIPT_NO_START_CODON,GACG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3784A>C|||||3784|WARNING_TRANSCRIPT_NO_START_CODON,GACC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3784_*3785delAGinsCC|||||3784|WARNING_TRANSCRIPT_NO_START_CODON,GAAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3785G>C|||||3785|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2461:1948,70,48,48,67,57,133,35:1948:63002:70,48,48,67,57,133,35:1249,803,708,1036,910,1875,507:0,-495.815,-5299.62,-529.806,-5264.1,-5340.23,-539.679,-5273.97,-5307.95,-5350.1,-513.622,-5247.91,-5281.9,-5291.77,-5318.33,-521.963,-5256.25,-5290.24,-5300.11,-5274.06,-5329.68,-458.325,-5192.61,-5226.6,-5236.47,-5210.41,-5218.75,-5243.16,-553.097,-5287.38,-5321.37,-5331.24,-5305.19,-5313.53,-5249.89,-5367.44
NC_045512.2	25350	.	CAGT	CT	9.354E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=349;CIGAR=1M2D1M;DP=3349;DPB=3175.5;DPRA=0;EPP=3.76316;EPPR=28.3979;GTI=0;LEN=2;MEANALT=7;MQM=49.7765;MQMR=52.6948;NS=1;NUMALT=1;ODDS=1420.92;PAIRED=0.994269;PAIREDR=0.978268;PAO=0;PQA=0;PQR=68;PRO=2;QA=11744;QR=105020;RO=2991;RPL=33;RPP=501.323;RPPR=873.505;RPR=316;RUN=1;SAF=180;SAP=3.76316;SAR=169;SRF=1504;SRP=3.22011;SRR=1487;TYPE=del;ANN=CT|frameshift_variant|HIGH|S|GU280_gp02|transcript|GU280_gp02|protein_coding|1/1|c.3789_3790delAG|p.Val1264fs|3789/3822|3789/3822|1263/1273||,CT|upstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.-42_-41delAG|||||42|,CT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-894_-893delAG|||||894|,CT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1172_-1171delAG|||||1172|,CT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1851_-1850delAG|||||1851|,CT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-2043_-2042delAG|||||2043|,CT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2405_-2404delAG|||||2405|,CT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2543_-2542delAG|||||2543|,CT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2923_-2922delAG|||||2923|,CT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4207_-4206delAG|||||4207|,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3796_*3797delAG|||||3796|,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4693_*4694delAG|||||4693|WARNING_TRANSCRIPT_NO_START_CODON,CT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3799_*3800delAG|||||3799|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3349:2991,349:2991:105020:349:11744:0,-32.0583,-8103.91
NC_045512.2	25439	.	A	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=409;CIGAR=1X;DP=4980;DPB=4980;DPRA=0;EPP=3.14303;EPPR=5.75601;GTI=0;LEN=1;MEANALT=3;MQM=42.0244;MQMR=50.0731;NS=1;NUMALT=1;ODDS=3047.76;PAIRED=0.99511;PAIREDR=0.99387;PAO=0;PQA=0;PQR=0;PRO=0;QA=14327;QR=161011;RO=4568;RPL=229;RPP=15.7577;RPPR=40.8133;RPR=180;RUN=1;SAF=205;SAP=3.01561;SAR=204;SRF=2235;SRP=7.57572;SRR=2333;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.47A>C|p.Lys16Thr|47/828|47/828|16/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-806A>C|||||806|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1084A>C|||||1084|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1763A>C|||||1763|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1955A>C|||||1955|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2317A>C|||||2317|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2455A>C|||||2455|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2835A>C|||||2835|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4119A>C|||||4119|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3884A>C|||||3884|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*55A>C|||||55|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4781A>C|||||4781|WARNING_TRANSCRIPT_NO_START_CODON,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3887A>C|||||3887|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4980:4568,409:4568:161011:409:14327:0,-430.196,-12414.4
NC_045512.2	25469	.	C	T	90198.9	.	AB=0.848337;ABP=4756.25;AC=1;AF=0.5;AN=2;AO=3826;CIGAR=1X;DP=4510;DPB=4510;DPRA=0;EPP=5.48258;EPPR=3.21348;GTI=0;LEN=1;MEANALT=1;MQM=48.1853;MQMR=53.5643;NS=1;NUMALT=1;ODDS=439.848;PAIRED=0.997909;PAIREDR=0.99269;PAO=0;PQA=0;PQR=0;PRO=0;QA=133615;QR=23901;RO=684;RPL=2121;RPP=101.229;RPPR=78.3007;RPR=1705;RUN=1;SAF=1915;SAP=3.01938;SAR=1911;SRF=341;SRP=3.023;SRR=343;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.77C>T|p.Ser26Leu|77/828|77/828|26/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-776C>T|||||776|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-1054C>T|||||1054|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1733C>T|||||1733|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1925C>T|||||1925|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2287C>T|||||2287|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2425C>T|||||2425|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2805C>T|||||2805|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-4089C>T|||||4089|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*3914C>T|||||3914|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*85C>T|||||85|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725310.1|protein_coding||c.*4811C>T|||||4811|WARNING_TRANSCRIPT_NO_START_CODON,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*3917C>T|||||3917|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4510:684,3826:684:23901:3826:133615:-9563.49,0,-731.026
NC_045512.2	25696	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=54;DPB=54;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=28.5;MQMR=51.6923;NS=1;NUMALT=1;ODDS=66.8874;PAIRED=0;PAIREDR=0.961538;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=1831;RO=52;RPL=2;RPP=7.35324;RPPR=11.1951;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=27;SRP=3.17734;SRR=25;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.304G>A|p.Glu102Lys|304/828|304/828|102/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-549G>A|||||549|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-827G>A|||||827|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1506G>A|||||1506|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1698G>A|||||1698|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2060G>A|||||2060|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2198G>A|||||2198|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2578G>A|||||2578|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3862G>A|||||3862|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4141G>A|||||4141|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*312G>A|||||312|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4144G>A|||||4144|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:54:52,2:52:1831:2:72:0,-12.7448,-153.498
NC_045512.2	25702	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=62;DPB=62;DPRA=0;EPP=5.18177;EPPR=3.33068;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.8525;NS=1;NUMALT=1;ODDS=85.2841;PAIRED=1;PAIREDR=0.967213;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2073;RO=61;RPL=0;RPP=5.18177;RPPR=15.8611;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=33;SRP=3.90025;SRR=28;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.310C>A|p.Pro104Thr|310/828|310/828|104/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-543C>A|||||543|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-821C>A|||||821|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1500C>A|||||1500|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1692C>A|||||1692|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2054C>A|||||2054|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2192C>A|||||2192|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2572C>A|||||2572|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3856C>A|||||3856|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4147C>A|||||4147|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*318C>A|||||318|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4150C>A|||||4150|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:62:61,1:61:2073:1:14:0,-17.2639,-174.471
NC_045512.2	25734	.	C	A	2.42589E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=68;DPB=68;DPRA=0;EPP=5.18177;EPPR=3.04271;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=50.6716;NS=1;NUMALT=1;ODDS=93.5095;PAIRED=1;PAIREDR=0.940299;PAO=0;PQA=0;PQR=0;PRO=0;QA=14;QR=2355;RO=67;RPL=0;RPP=5.18177;RPPR=23.2666;RPR=1;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=35;SRP=3.30199;SRR=32;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.342C>A|p.Phe114Leu|342/828|342/828|114/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-511C>A|||||511|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-789C>A|||||789|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1468C>A|||||1468|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1660C>A|||||1660|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2022C>A|||||2022|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2160C>A|||||2160|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2540C>A|||||2540|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3824C>A|||||3824|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4179C>A|||||4179|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*350C>A|||||350|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4182C>A|||||4182|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:68:67,1:67:2355:1:14:0,-19.07,-196.772
NC_045512.2	25750	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=74;DPB=74;DPRA=0;EPP=3.0103;EPPR=3.13094;GTI=0;LEN=1;MEANALT=1;MQM=54.5;MQMR=51.2222;NS=1;NUMALT=1;ODDS=86.3627;PAIRED=1;PAIREDR=0.944444;PAO=0;PQA=0;PQR=0;PRO=0;QA=72;QR=2546;RO=72;RPL=2;RPP=7.35324;RPPR=6.02623;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=38;SRP=3.49285;SRR=34;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.358T>C|p.Phe120Leu|358/828|358/828|120/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-495T>C|||||495|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-773T>C|||||773|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1452T>C|||||1452|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1644T>C|||||1644|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-2006T>C|||||2006|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2144T>C|||||2144|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2524T>C|||||2524|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3808T>C|||||3808|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4195T>C|||||4195|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*366T>C|||||366|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4198T>C|||||4198|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:74:72,2:72:2546:2:72:0,-15.458,-208.988
NC_045512.2	25785	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=10;CIGAR=1X;DP=90;DPB=90;DPRA=0;EPP=3.0103;EPPR=3.11887;GTI=0;LEN=1;MEANALT=1;MQM=41.7;MQMR=51.4625;NS=1;NUMALT=1;ODDS=45.1658;PAIRED=1;PAIREDR=0.975;PAO=0;PQA=0;PQR=0;PRO=0;QA=356;QR=2776;RO=80;RPL=2;RPP=10.8276;RPPR=4.74748;RPR=8;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=41;SRP=3.11887;SRR=39;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.393G>T|p.Trp131Cys|393/828|393/828|131/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-460G>T|||||460|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-738G>T|||||738|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1417G>T|||||1417|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1609G>T|||||1609|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1971G>T|||||1971|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2109G>T|||||2109|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2489G>T|||||2489|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3773G>T|||||3773|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4230G>T|||||4230|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*401G>T|||||401|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4233G>T|||||4233|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:90:80,10:80:2776:10:356:0,-0.705101,-211.729
NC_045512.2	25797	.	CAAAAACCCAT	CAAAAAACCCAT,CAAAAACCCAC	73.745	.	AB=0.1875,0.0208333;ABP=84.4405,194.462;AC=1,0;AF=0.5,0;AN=2;AO=18,2;CIGAR=1M1I10M,10M1X;DP=96;DPB=97.6364;DPRA=0,0;EPP=3.0103,3.0103;EPPR=3.12459;GTI=0;LEN=1,1;MEANALT=2,2;MQM=51.2778,55.5;MQMR=49.3684;NS=1;NUMALT=2;ODDS=16.9804;PAIRED=1,1;PAIREDR=0.973684;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=555,72;QR=2648;RO=76;RPL=8,2;RPP=3.49285,7.35324;RPPR=3.46745;RPR=10,0;RUN=1,1;SAF=9,1;SAP=3.0103,3.0103;SAR=9,1;SRF=39;SRP=3.12459;SRR=37;TYPE=ins,snp;ANN=CAAAAAACCCAT|frameshift_variant|HIGH|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.410dupA|p.Asn137fs|411/828|411/828|137/275||,CAAAAACCCAC|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.415T>C|p.Leu139Leu|415/828|415/828|139/275||,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-443dupA|||||442|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-438T>C|||||438|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-721dupA|||||720|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-716T>C|||||716|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1400dupA|||||1399|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1395T>C|||||1395|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1592dupA|||||1591|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1587T>C|||||1587|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1954dupA|||||1953|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1949T>C|||||1949|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2092dupA|||||2091|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2087T>C|||||2087|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2472dupA|||||2471|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2467T>C|||||2467|,CAAAAAACCCAT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3756dupA|||||3755|,CAAAAACCCAC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3751T>C|||||3751|,CAAAAAACCCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4247dupA|||||4248|,CAAAAACCCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4252T>C|||||4252|,CAAAAAACCCAT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*418dupA|||||419|,CAAAAACCCAC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*423T>C|||||423|,CAAAAAACCCAT|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4250dupA|||||4251|WARNING_TRANSCRIPT_NO_START_CODON,CAAAAACCCAC|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4255T>C|||||4255|WARNING_TRANSCRIPT_NO_START_CODON;LOF=(ORF3a|GU280_gp03|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/1:96:76,18,2:76:2648:18,2:555,72:-20.9576,0,-190.254,-37.9662,-189.807,-233.088
NC_045512.2	25811	.	T	A	1.76315E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.0103;EPPR=3.21602;GTI=0;LEN=1;MEANALT=1;MQM=54;MQMR=49.9368;NS=1;NUMALT=1;ODDS=118.555;PAIRED=1;PAIREDR=0.978947;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=3323;RO=95;RPL=2;RPP=7.35324;RPPR=5.77607;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=49;SRP=3.21602;SRR=46;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.419T>A|p.Leu140His|419/828|419/828|140/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-434T>A|||||434|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-712T>A|||||712|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1391T>A|||||1391|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1583T>A|||||1583|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1945T>A|||||1945|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2083T>A|||||2083|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2463T>A|||||2463|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3747T>A|||||3747|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4256T>A|||||4256|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*427T>A|||||427|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4259T>A|||||4259|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:97:95,2:95:3323:2:68:0,-22.7518,-268.02
NC_045512.2	25831	.	C	T	3.18727E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=4;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=30.75;MQMR=54.1733;NS=1;NUMALT=1;ODDS=86.1664;PAIRED=1;PAIREDR=0.973333;PAO=0;PQA=0;PQR=0;PRO=0;QA=144;QR=2659;RO=75;RPL=4;RPP=11.6962;RPPR=6.51361;RPR=0;RUN=1;SAF=2;SAP=3.0103;SAR=2;SRF=38;SRP=3.03925;SRR=37;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.439C>T|p.Leu147Phe|439/828|439/828|147/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-414C>T|||||414|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-692C>T|||||692|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1371C>T|||||1371|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1563C>T|||||1563|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1925C>T|||||1925|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-2063C>T|||||2063|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2443C>T|||||2443|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3727C>T|||||3727|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4276C>T|||||4276|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*447C>T|||||447|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4279C>T|||||4279|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:79:75,4:75:2659:4:144:0,-15.761,-225.561
NC_045512.2	26042	.	CTCAA	TTGAG	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X1M1X1M1X;DP=1484;DPB=1485;DPRA=0;EPP=3.0103;EPPR=3.08455;GTI=0;LEN=5;MEANALT=5;MQM=43.3182;MQMR=53.2568;NS=1;NUMALT=1;ODDS=1592.01;PAIRED=1;PAIREDR=0.993719;PAO=6;PQA=136;PQR=32;PRO=1;QA=1544;QR=50198;RO=1433;RPL=22;RPP=3.0103;RPPR=7.93362;RPR=22;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=738;SRP=5.81215;SRR=695;TYPE=complex;ANN=TTGAG|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.650_654delCTCAAinsTTGAG|p.ThrGln217IleGlu|650/828|650/828|217/275||,TTGAG|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-203_-199delCTCAAinsTTGAG|||||203|,TTGAG|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-481_-477delCTCAAinsTTGAG|||||481|,TTGAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1160_-1156delCTCAAinsTTGAG|||||1160|,TTGAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1352_-1348delCTCAAinsTTGAG|||||1352|,TTGAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1714_-1710delCTCAAinsTTGAG|||||1714|,TTGAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1852_-1848delCTCAAinsTTGAG|||||1852|,TTGAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2232_-2228delCTCAAinsTTGAG|||||2232|,TTGAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3516_-3512delCTCAAinsTTGAG|||||3516|,TTGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4487_*4491delCTCAAinsTTGAG|||||4487|,TTGAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*658_*662delCTCAAinsTTGAG|||||658|,TTGAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4490_*4494delCTCAAinsTTGAG|||||4490|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1484:1433,44:1433:50198:44:1544:0,-326.758,-4246.55
NC_045512.2	26057	.	A	C	1.04572E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1X;DP=1482;DPB=1482;DPRA=0;EPP=3.15506;EPPR=3.02364;GTI=0;LEN=1;MEANALT=2;MQM=47.2667;MQMR=52.9747;NS=1;NUMALT=1;ODDS=1903.72;PAIRED=1;PAIREDR=0.995904;PAO=0;PQA=0;PQR=0;PRO=0;QA=421;QR=49584;RO=1465;RPL=11;RPP=10.1038;RPPR=12.7352;RPR=4;RUN=1;SAF=9;SAP=4.31318;SAR=6;SRF=728;SRP=3.13036;SRR=737;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.665A>C|p.Asp222Ala|665/828|665/828|222/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-188A>C|||||188|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-466A>C|||||466|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1145A>C|||||1145|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1337A>C|||||1337|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1699A>C|||||1699|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1837A>C|||||1837|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2217A>C|||||2217|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3501A>C|||||3501|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4502A>C|||||4502|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*673A>C|||||673|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4505A>C|||||4505|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1482:1465,15:1465:49584:15:421:0,-411.753,-4275.18
NC_045512.2	26069	.	A	G	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1483;DPB=1483;DPRA=0;EPP=3.0103;EPPR=3.1302;GTI=0;LEN=1;MEANALT=1;MQM=42.8125;MQMR=52.7764;NS=1;NUMALT=1;ODDS=1886.92;PAIRED=0.875;PAIREDR=0.99591;PAO=0;PQA=0;PQR=0;PRO=0;QA=576;QR=51331;RO=1467;RPL=16;RPP=37.7539;RPPR=4.08938;RPR=0;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=725;SRP=3.43808;SRR=742;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.677A>G|p.Glu226Gly|677/828|677/828|226/275||,G|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-176A>G|||||176|,G|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-454A>G|||||454|,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1133A>G|||||1133|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1325A>G|||||1325|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1687A>G|||||1687|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1825A>G|||||1825|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2205A>G|||||2205|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3489A>G|||||3489|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4514A>G|||||4514|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*685A>G|||||685|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4517A>G|||||4517|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1483:1467,16:1467:51331:16:576:0,-402.204,-4405.87
NC_045512.2	26089	.	T	A	2.41553E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1477;DPB=1477;DPRA=0;EPP=3.13803;EPPR=4.17635;GTI=0;LEN=1;MEANALT=1;MQM=41.7647;MQMR=52.7048;NS=1;NUMALT=1;ODDS=1870.29;PAIRED=1;PAIREDR=0.994521;PAO=0;PQA=0;PQR=0;PRO=0;QA=586;QR=49501;RO=1460;RPL=16;RPP=31.7504;RPPR=8.36462;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=746;SRP=4.53331;SRR=714;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.697T>A|p.Tyr233Asn|697/828|697/828|233/275||,A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-156T>A|||||156|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-434T>A|||||434|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1113T>A|||||1113|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1305T>A|||||1305|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1667T>A|||||1667|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1805T>A|||||1805|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2185T>A|||||2185|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3469T>A|||||3469|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4534T>A|||||4534|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*705T>A|||||705|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4537T>A|||||4537|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1477:1460,17:1460:49501:17:586:0,-399.573,-4252.67
NC_045512.2	26108	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1558;DPB=1558;DPRA=0;EPP=3.0103;EPPR=3.3708;GTI=0;LEN=1;MEANALT=1;MQM=51.8125;MQMR=52.0246;NS=1;NUMALT=1;ODDS=1968.1;PAIRED=1;PAIREDR=0.990272;PAO=0;PQA=0;PQR=0;PRO=0;QA=553;QR=52400;RO=1542;RPL=8;RPP=3.0103;RPPR=11.1442;RPR=8;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=768;SRP=3.061;SRR=774;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.716A>T|p.Glu239Val|716/828|716/828|239/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-137A>T|||||137|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-415A>T|||||415|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1094A>T|||||1094|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1286A>T|||||1286|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1648A>T|||||1648|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1786A>T|||||1786|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2166A>T|||||2166|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3450A>T|||||3450|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4553A>T|||||4553|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*724A>T|||||724|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4556A>T|||||4556|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1558:1542,16:1542:52400:16:553:0,-419.335,-4448.58
NC_045512.2	26141	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1X;DP=1542;DPB=1542;DPRA=0;EPP=3.13803;EPPR=3.06166;GTI=0;LEN=1;MEANALT=3;MQM=30.8235;MQMR=52.1393;NS=1;NUMALT=1;ODDS=1984.85;PAIRED=0.764706;PAIREDR=0.996058;PAO=0;PQA=0;PQR=0;PRO=0;QA=551;QR=50688;RO=1522;RPL=16;RPP=31.7504;RPPR=7.17062;RPR=1;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=758;SRP=3.06166;SRR=764;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.749A>T|p.Asp250Val|749/828|749/828|250/275||,T|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-104A>T|||||104|,T|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-382A>T|||||382|,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1061A>T|||||1061|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1253A>T|||||1253|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1615A>T|||||1615|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1753A>T|||||1753|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2133A>T|||||2133|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3417A>T|||||3417|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4586A>T|||||4586|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*757A>T|||||757|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4589A>T|||||4589|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1542:1522,17:1522:50688:17:551:0,-430.965,-4315.93
NC_045512.2	26145	.	T	C	4.23704E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=20;CIGAR=1X;DP=1538;DPB=1538;DPRA=0;EPP=3.44459;EPPR=3.21656;GTI=0;LEN=1;MEANALT=2;MQM=47.8;MQMR=51.9208;NS=1;NUMALT=1;ODDS=1909.48;PAIRED=1;PAIREDR=0.991425;PAO=0;PQA=0;PQR=0;PRO=0;QA=678;QR=48753;RO=1516;RPL=14;RPP=9.95901;RPPR=34.3849;RPR=6;RUN=1;SAF=9;SAP=3.44459;SAR=11;SRF=758;SRP=3.0103;SRR=758;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding|1/1|c.753T>C|p.Gly251Gly|753/828|753/828|251/275||,C|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-100T>C|||||100|,C|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-378T>C|||||378|,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-1057T>C|||||1057|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1249T>C|||||1249|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1611T>C|||||1611|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1749T>C|||||1749|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2129T>C|||||2129|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3413T>C|||||3413|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4590T>C|||||4590|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*761T>C|||||761|,C|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4593T>C|||||4593|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1538:1516,20:1516:48753:20:678:0,-407.159,-4121.98
NC_045512.2	26221	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=32;CIGAR=1X;DP=2217;DPB=2217;DPRA=0;EPP=3.28173;EPPR=3.583;GTI=0;LEN=1;MEANALT=2;MQM=48.5312;MQMR=50.4084;NS=1;NUMALT=1;ODDS=2709.72;PAIRED=1;PAIREDR=0.995879;PAO=0;PQA=0;PQR=0;PRO=0;QA=1101;QR=76749;RO=2184;RPL=15;RPP=3.28173;RPPR=759.033;RPR=17;RUN=1;SAF=16;SAP=3.0103;SAR=16;SRF=1104;SRP=3.583;SRR=1080;TYPE=snp;ANN=A|upstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.-24G>A|||||24|,A|upstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.-302G>A|||||302|,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-981G>A|||||981|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1173G>A|||||1173|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1535G>A|||||1535|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1673G>A|||||1673|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-2053G>A|||||2053|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3337G>A|||||3337|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4666G>A|||||4666|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*837G>A|||||837|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1G>A|||||1|,A|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4669G>A|||||4669|WARNING_TRANSCRIPT_NO_START_CODON,A|intergenic_region|MODIFIER|ORF3a-E|GU280_gp03-GU280_gp04|intergenic_region|GU280_gp03-GU280_gp04|||n.26221G>A||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2217:2184,32:2184:76749:32:1101:0,-576.661,-6377.21
NC_045512.2	26533	.	C	T	6.38867E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=52;CIGAR=1X;DP=2958;DPB=2958;DPRA=0;EPP=9.02361;EPPR=16.2327;GTI=0;LEN=1;MEANALT=2;MQM=32.3077;MQMR=51.4386;NS=1;NUMALT=1;ODDS=3622.99;PAIRED=0.692308;PAIREDR=0.993804;PAO=0;PQA=0;PQR=0;PRO=0;QA=1770;QR=101214;RO=2905;RPL=12;RPP=35.7494;RPPR=3.28015;RPR=40;RUN=1;SAF=18;SAP=13.7006;SAR=34;SRF=1471;SRP=4.03362;SRR=1434;TYPE=snp;ANN=T|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.11C>T|p.Ser4Phe|11/669|11/669|4/222||,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-669C>T|||||669|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-861C>T|||||861|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1223C>T|||||1223|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1361C>T|||||1361|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1741C>T|||||1741|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3025C>T|||||3025|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4978C>T|||||4978|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1149C>T|||||1149|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*313C>T|||||313|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*61C>T|||||61|,T|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4981C>T|||||4981|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2958:2905,52:2905:101214:52:1770:0,-785.764,-8554.41
NC_045512.2	26542	.	CTAT	ATAG	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=131;CIGAR=1X2M1X;DP=2947;DPB=2947;DPRA=0;EPP=3.15949;EPPR=17.7373;GTI=0;LEN=4;MEANALT=5;MQM=38.9771;MQMR=51.3038;NS=1;NUMALT=1;ODDS=2841.52;PAIRED=0.755725;PAIREDR=0.99359;PAO=1;PQA=32;PQR=0;PRO=0;QA=4580;QR=99098;RO=2808;RPL=36;RPP=60.7118;RPPR=16.0793;RPR=95;RUN=1;SAF=65;SAP=3.02688;SAR=66;SRF=1418;SRP=3.61658;SRR=1390;TYPE=complex;ANN=ATAG|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.20_23delCTATinsATAG|p.ThrIle7AsnSer|20/669|20/669|7/222||,ATAG|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-660_-657delCTATinsATAG|||||660|,ATAG|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-852_-849delCTATinsATAG|||||852|,ATAG|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1214_-1211delCTATinsATAG|||||1214|,ATAG|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1352_-1349delCTATinsATAG|||||1352|,ATAG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1732_-1729delCTATinsATAG|||||1732|,ATAG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3016_-3013delCTATinsATAG|||||3016|,ATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4987_*4990delCTATinsATAG|||||4987|,ATAG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1158_*1161delCTATinsATAG|||||1158|,ATAG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*322_*325delCTATinsATAG|||||322|,ATAG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*70_*73delCTATinsATAG|||||70|,ATAG|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|YP_009725311.1|protein_coding||c.*4990_*4993delCTATinsATAG|||||4990|WARNING_TRANSCRIPT_NO_START_CODON	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2947:2808,131:2808:99098:131:4580:0,-569.035,-8155.39
NC_045512.2	26554	.	A	G	1.18733E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=40;CIGAR=1X;DP=3289;DPB=3289;DPRA=0;EPP=3.22745;EPPR=16.114;GTI=0;LEN=1;MEANALT=2;MQM=39.325;MQMR=50.3211;NS=1;NUMALT=1;ODDS=4149.91;PAIRED=0.65;PAIREDR=0.9883;PAO=0;PQA=0;PQR=0;PRO=0;QA=1381;QR=113659;RO=3248;RPL=10;RPP=24.725;RPPR=189.393;RPR=30;RUN=1;SAF=21;SAP=3.22745;SAR=19;SRF=1620;SRP=3.05309;SRR=1628;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.32A>G|p.Glu11Gly|32/669|32/669|11/222||,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-648A>G|||||648|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-840A>G|||||840|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1202A>G|||||1202|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1340A>G|||||1340|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1720A>G|||||1720|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-3004A>G|||||3004|,G|downstream_gene_variant|MODIFIER|ORF1ab|GU280_gp01|transcript|GU280_gp01|protein_coding||c.*4999A>G|||||4999|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1170A>G|||||1170|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*334A>G|||||334|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*82A>G|||||82|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3289:3248,40:3248:113659:40:1381:0,-898.198,-9489.65
NC_045512.2	26611	.	C	G	0.0	.	AB=0.134243;ABP=4858.94;AC=1;AF=0.5;AN=2;AO=561;CIGAR=1X;DP=4179;DPB=4179;DPRA=0;EPP=3.19997;EPPR=9.88753;GTI=0;LEN=1;MEANALT=2;MQM=48.8645;MQMR=51.8661;NS=1;NUMALT=1;ODDS=409.84;PAIRED=0.982175;PAIREDR=0.986999;PAO=0;PQA=0;PQR=0;PRO=0;QA=19867;QR=126762;RO=3615;RPL=206;RPP=88.9441;RPPR=79.5669;RPR=355;RUN=1;SAF=285;SAP=3.32383;SAR=276;SRF=1845;SRP=6.38915;SRR=1770;TYPE=snp;ANN=G|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.89C>G|p.Thr30Arg|89/669|89/669|30/222||,G|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-591C>G|||||591|,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-783C>G|||||783|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1145C>G|||||1145|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1283C>G|||||1283|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1663C>G|||||1663|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2947C>G|||||2947|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1227C>G|||||1227|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*391C>G|||||391|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*139C>G|||||139|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4179:3615,561:3615:126762:561:19867:-380.436,0,-9637.08
NC_045512.2	26705	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=193;CIGAR=1X;DP=4508;DPB=4508;DPRA=0;EPP=3.29158;EPPR=3.62734;GTI=0;LEN=1;MEANALT=3;MQM=49.8187;MQMR=52.6518;NS=1;NUMALT=1;ODDS=4146.13;PAIRED=0.994819;PAIREDR=0.992577;PAO=0;PQA=0;PQR=0;PRO=0;QA=6785;QR=152705;RO=4311;RPL=116;RPP=20.1233;RPPR=31.3029;RPR=77;RUN=1;SAF=97;SAP=3.02155;SAR=96;SRF=2179;SRP=4.12298;SRR=2132;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.183T>C|p.Thr61Thr|183/669|183/669|61/222||,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-497T>C|||||497|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-689T>C|||||689|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-1051T>C|||||1051|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1189T>C|||||1189|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1569T>C|||||1569|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2853T>C|||||2853|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1321T>C|||||1321|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*485T>C|||||485|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*233T>C|||||233|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4508:4311,193:4311:152705:193:6785:0,-781.83,-12614.8
NC_045512.2	26767	.	T	C	67526.2	.	AB=0.695281;ABP=1322.65;AC=1;AF=0.5;AN=2;AO=2770;CIGAR=1X;DP=3984;DPB=3984;DPRA=0;EPP=6.02371;EPPR=4.62278;GTI=0;LEN=1;MEANALT=2;MQM=50.2946;MQMR=53.2954;NS=1;NUMALT=1;ODDS=5439.65;PAIRED=0.998917;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=96278;QR=42353;RO=1212;RPL=1420;RPP=6.85153;RPPR=11.2949;RPR=1350;RUN=1;SAF=1358;SAP=5.29623;SAR=1412;SRF=599;SRP=3.36146;SRR=613;TYPE=snp;ANN=C|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.245T>C|p.Ile82Thr|245/669|245/669|82/222||,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-435T>C|||||435|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-627T>C|||||627|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-989T>C|||||989|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1127T>C|||||1127|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1507T>C|||||1507|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2791T>C|||||2791|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1383T>C|||||1383|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*547T>C|||||547|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*295T>C|||||295|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3984:1212,2770:1212:42353:2770:96278:-6898.83,0,-2508.19
NC_045512.2	26837	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=44;CIGAR=1X;DP=3100;DPB=3100;DPRA=0;EPP=4.78696;EPPR=3.17023;GTI=0;LEN=1;MEANALT=2;MQM=50.3409;MQMR=51.6887;NS=1;NUMALT=1;ODDS=3775.78;PAIRED=1;PAIREDR=0.997709;PAO=0;PQA=0;PQR=0;PRO=0;QA=1554;QR=105912;RO=3055;RPL=29;RPP=12.6832;RPPR=391.189;RPR=15;RUN=1;SAF=22;SAP=3.0103;SAR=22;SRF=1491;SRP=6.79812;SRR=1564;TYPE=snp;ANN=C|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.315T>C|p.Arg105Arg|315/669|315/669|105/222||,C|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-365T>C|||||365|,C|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-557T>C|||||557|,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-919T>C|||||919|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-1057T>C|||||1057|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1437T>C|||||1437|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2721T>C|||||2721|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1453T>C|||||1453|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*617T>C|||||617|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*365T>C|||||365|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3100:3055,44:3055:105912:44:1554:0,-800.061,-8955.04
NC_045512.2	27059	.	C	T	3.69338E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=299;CIGAR=1X;DP=5267;DPB=5267;DPRA=0;EPP=3.88906;EPPR=4.10568;GTI=0;LEN=1;MEANALT=3;MQM=45.204;MQMR=51.677;NS=1;NUMALT=1;ODDS=4275.32;PAIRED=0.986622;PAIREDR=0.993341;PAO=0;PQA=0;PQR=0;PRO=0;QA=10578;QR=173846;RO=4956;RPL=185;RPP=39.6203;RPPR=25.3893;RPR=114;RUN=1;SAF=148;SAP=3.07566;SAR=151;SRF=2474;SRP=3.03834;SRR=2482;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.537C>T|p.Tyr179Tyr|537/669|537/669|179/222||,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-143C>T|||||143|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-335C>T|||||335|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-697C>T|||||697|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-835C>T|||||835|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1215C>T|||||1215|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2499C>T|||||2499|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1675C>T|||||1675|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*839C>T|||||839|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*587C>T|||||587|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5267:4956,299:4956:173846:299:10578:0,-761.739,-14058.3
NC_045512.2	27115	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=184;CIGAR=1X;DP=4546;DPB=4546;DPRA=0;EPP=3.0103;EPPR=8.93164;GTI=0;LEN=1;MEANALT=2;MQM=48.6087;MQMR=51.3668;NS=1;NUMALT=1;ODDS=4300.67;PAIRED=1;PAIREDR=0.990131;PAO=0;PQA=0;PQR=0;PRO=0;QA=6564;QR=151056;RO=4357;RPL=90;RPP=3.19912;RPPR=3.37362;RPR=94;RUN=1;SAF=90;SAP=3.19912;SAR=94;SRF=2144;SRP=5.38312;SRR=2213;TYPE=snp;ANN=A|missense_variant|MODERATE|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.593G>A|p.Arg198His|593/669|593/669|198/222||,A|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-87G>A|||||87|,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-279G>A|||||279|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-641G>A|||||641|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-779G>A|||||779|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1159G>A|||||1159|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2443G>A|||||2443|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1731G>A|||||1731|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*895G>A|||||895|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*643G>A|||||643|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4546:4357,184:4357:151056:184:6564:0,-827.983,-12351.2
NC_045512.2	27143	.	C	T	1.70204E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=272;CIGAR=1X;DP=4401;DPB=4401;DPRA=0;EPP=3.2977;EPPR=6.99475;GTI=0;LEN=1;MEANALT=3;MQM=47.0993;MQMR=50.1321;NS=1;NUMALT=1;ODDS=3329.47;PAIRED=0.992647;PAIREDR=0.987394;PAO=0;PQA=0;PQR=0;PRO=0;QA=9558;QR=143551;RO=4125;RPL=154;RPP=13.3567;RPPR=237.208;RPR=118;RUN=1;SAF=133;SAP=3.2977;SAR=139;SRF=2054;SRP=3.16243;SRR=2071;TYPE=snp;ANN=T|synonymous_variant|LOW|M|GU280_gp05|transcript|GU280_gp05|protein_coding|1/1|c.621C>T|p.Asn207Asn|621/669|621/669|207/222||,T|upstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.-59C>T|||||59|,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-251C>T|||||251|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-613C>T|||||613|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-751C>T|||||751|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-1131C>T|||||1131|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2415C>T|||||2415|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1759C>T|||||1759|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*923C>T|||||923|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*671C>T|||||671|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4401:4125,272:4125:143551:272:9558:0,-556.834,-11234.5
NC_045512.2	27285	.	T	A	8.19702E-15	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=31;CIGAR=1X;DP=2885;DPB=2885;DPRA=0;EPP=3.08035;EPPR=5.2305;GTI=0;LEN=1;MEANALT=2;MQM=45;MQMR=53.3229;NS=1;NUMALT=1;ODDS=3664.07;PAIRED=1;PAIREDR=0.990182;PAO=0;PQA=0;PQR=0;PRO=0;QA=1108;QR=100423;RO=2852;RPL=0;RPP=70.3259;RPPR=3.99706;RPR=31;RUN=1;SAF=16;SAP=3.08035;SAR=15;SRF=1471;SRP=9.17753;SRR=1381;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.84T>A|p.Asn28Lys|84/186|84/186|28/61||,A|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-109T>A|||||109|,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-471T>A|||||471|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-609T>A|||||609|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-989T>A|||||989|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2273T>A|||||2273|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1901T>A|||||1901|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1065T>A|||||1065|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*813T>A|||||813|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*94T>A|||||94|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2885:2852,31:2852:100423:31:1108:0,-783.645,-8676.19
NC_045512.2	27291	.	TTACA	TA	1.11018E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=61;CIGAR=1M3D1M;DP=2674;DPB=2637.6;DPRA=0;EPP=3.0459;EPPR=3.01363;GTI=0;LEN=3;MEANALT=4;MQM=52.6721;MQMR=53.3507;NS=1;NUMALT=1;ODDS=3002.68;PAIRED=1;PAIREDR=0.989639;PAO=0.5;PQA=10.5;PQR=10.5;PRO=0.5;QA=2128;QR=92098;RO=2606;RPL=41;RPP=18.709;RPPR=33.0909;RPR=20;RUN=1;SAF=31;SAP=3.0459;SAR=30;SRF=1312;SRP=3.28028;SRR=1294;TYPE=del;ANN=TA|conservative_inframe_deletion|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.91_93delTAC|p.Tyr31del|91/186|91/186|31/61||,TA|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-102_-100delTAC|||||102|,TA|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-464_-462delTAC|||||464|,TA|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-602_-600delTAC|||||602|,TA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-982_-980delTAC|||||982|,TA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2266_-2264delTAC|||||2266|,TA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1908_*1910delTAC|||||1908|,TA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1072_*1074delTAC|||||1072|,TA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*820_*822delTAC|||||820|,TA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*101_*103delTAC|||||101|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2674:2606,61:2606:92098:61:2128:0,-619.622,-7867.5
NC_045512.2	27335	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=78;CIGAR=1X;DP=3108;DPB=3108;DPRA=0;EPP=4.01252;EPPR=6.42569;GTI=0;LEN=1;MEANALT=2;MQM=44.7051;MQMR=53.372;NS=1;NUMALT=1;ODDS=3467.05;PAIRED=0.948718;PAIREDR=0.991411;PAO=0;PQA=0;PQR=0;PRO=0;QA=2703;QR=106229;RO=3027;RPL=39;RPP=3.0103;RPPR=10.3282;RPR=39;RUN=1;SAF=41;SAP=3.45573;SAR=37;SRF=1522;SRP=3.21762;SRR=1505;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.134C>T|p.Thr45Ile|134/186|134/186|45/61||,T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-59C>T|||||59|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-421C>T|||||421|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-559C>T|||||559|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-939C>T|||||939|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2223C>T|||||2223|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1951C>T|||||1951|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1115C>T|||||1115|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*863C>T|||||863|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*144C>T|||||144|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3108:3027,78:3027:106229:78:2703:0,-722.646,-9061.78
NC_045512.2	27344	.	AA	TT	1.55256E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=2X;DP=3040;DPB=3040.5;DPRA=0;EPP=3.21602;EPPR=5.24228;GTI=0;LEN=2;MEANALT=3;MQM=45.7684;MQMR=53.5352;NS=1;NUMALT=1;ODDS=3202.24;PAIRED=0.978947;PAIREDR=0.991505;PAO=1;PQA=36;PQR=0;PRO=0;QA=3335;QR=103633;RO=2943;RPL=40;RPP=8.15326;RPPR=3.01104;RPR=55;RUN=1;SAF=47;SAP=3.03316;SAR=48;SRF=1464;SRP=3.17631;SRR=1479;TYPE=complex;ANN=TT|missense_variant|MODERATE|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.143_144delAAinsTT|p.Lys48Ile|143/186|143/186|48/61||,TT|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-50_-49delAAinsTT|||||50|,TT|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-412_-411delAAinsTT|||||412|,TT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-550_-549delAAinsTT|||||550|,TT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-930_-929delAAinsTT|||||930|,TT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2214_-2213delAAinsTT|||||2214|,TT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1960_*1961delAAinsTT|||||1960|,TT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1124_*1125delAAinsTT|||||1124|,TT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*872_*873delAAinsTT|||||872|,TT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*153_*154delAAinsTT|||||153|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3040:2943,95:2943:103633:95:3335:0,-652.573,-8806.08
NC_045512.2	27354	.	A	G	1.21024E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=68;CIGAR=1X;DP=3037;DPB=3037;DPRA=0;EPP=4.1599;EPPR=3.54384;GTI=0;LEN=1;MEANALT=2;MQM=44.5;MQMR=53.3401;NS=1;NUMALT=1;ODDS=3477.58;PAIRED=0.970588;PAIREDR=0.990226;PAO=0;PQA=0;PQR=0;PRO=0;QA=2347;QR=103746;RO=2967;RPL=33;RPP=3.13803;RPPR=3.01689;RPR=35;RUN=1;SAF=32;SAP=3.52123;SAR=36;SRF=1482;SRP=3.01689;SRR=1485;TYPE=snp;ANN=G|synonymous_variant|LOW|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding|1/1|c.153A>G|p.Gln51Gln|153/186|153/186|51/61||,G|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-40A>G|||||40|,G|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-402A>G|||||402|,G|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-540A>G|||||540|,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-920A>G|||||920|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2204A>G|||||2204|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*1970A>G|||||1970|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1134A>G|||||1134|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*882A>G|||||882|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*163A>G|||||163|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3037:2967,68:2967:103746:68:2347:0,-731.506,-8865.91
NC_045512.2	27393	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=73;CIGAR=1X;DP=2871;DPB=2871;DPRA=0;EPP=3.04005;EPPR=4.51494;GTI=0;LEN=1;MEANALT=3;MQM=53.1233;MQMR=53.4395;NS=1;NUMALT=1;ODDS=3121.07;PAIRED=1;PAIREDR=0.993916;PAO=0;PQA=0;PQR=0;PRO=0;QA=2586;QR=97778;RO=2794;RPL=38;RPP=3.27802;RPPR=84.5967;RPR=35;RUN=1;SAF=36;SAP=3.04005;SAR=37;SRF=1368;SRP=5.62477;SRR=1426;TYPE=snp;ANN=T|upstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.-1C>T|||||1|,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-363C>T|||||363|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-501C>T|||||501|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-881C>T|||||881|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2165C>T|||||2165|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2009C>T|||||2009|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1173C>T|||||1173|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*921C>T|||||921|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*202C>T|||||202|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*6C>T|||||6|,T|intergenic_region|MODIFIER|ORF6-ORF7a|GU280_gp06-GU280_gp07|intergenic_region|GU280_gp06-GU280_gp07|||n.27393C>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2871:2794,73:2794:97778:73:2586:0,-633.624,-8285.14
NC_045512.2	27527	.	C	T	20959.5	.	AB=0.321568;ABP=998.011;AC=1;AF=0.5;AN=2;AO=1157;CIGAR=1X;DP=3598;DPB=3598;DPRA=0;EPP=3.16232;EPPR=3.97985;GTI=0;LEN=1;MEANALT=2;MQM=48.0026;MQMR=50.8844;NS=1;NUMALT=1;ODDS=4826.11;PAIRED=0.994814;PAIREDR=0.99672;PAO=0;PQA=0;PQR=0;PRO=0;QA=40472;QR=84380;RO=2439;RPL=514;RPP=34.2423;RPPR=4.81318;RPR=643;RUN=1;SAF=592;SAP=4.3785;SAR=565;SRF=1214;SRP=3.11803;SRR=1225;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.134C>T|p.Pro45Leu|134/366|134/366|45/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-229C>T|||||229|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-367C>T|||||367|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-747C>T|||||747|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-2031C>T|||||2031|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2143C>T|||||2143|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1307C>T|||||1307|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1055C>T|||||1055|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*336C>T|||||336|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*140C>T|||||140|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3598:2439,1157:2439:84380:1157:40472:-2209.43,0,-6034.2
NC_045512.2	27566	.	G	T	5352.15	.	AB=0.189077;ABP=3231.63;AC=1;AF=0.5;AN=2;AO=727;CIGAR=1X;DP=3845;DPB=3845;DPRA=0;EPP=3.08497;EPPR=3.59619;GTI=0;LEN=1;MEANALT=2;MQM=46.6768;MQMR=50.3141;NS=1;NUMALT=1;ODDS=1232.38;PAIRED=0.997249;PAIREDR=0.983959;PAO=0;PQA=0;PQR=0;PRO=0;QA=25485;QR=108948;RO=3117;RPL=374;RPP=4.32752;RPPR=10.1169;RPR=353;RUN=1;SAF=373;SAP=4.08857;SAR=354;SRF=1591;SRP=5.95367;SRR=1526;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.173G>T|p.Cys58Phe|173/366|173/366|58/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-190G>T|||||190|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-328G>T|||||328|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-708G>T|||||708|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1992G>T|||||1992|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2182G>T|||||2182|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1346G>T|||||1346|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1094G>T|||||1094|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*375G>T|||||375|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*179G>T|||||179|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3845:3117,727:3117:108948:727:25485:-891.399,0,-7962.88
NC_045512.2	27607	.	A	T	5075.59	.	AB=0.18089;ABP=3640.94;AC=1;AF=0.5;AN=2;AO=744;CIGAR=1X;DP=4113;DPB=4113;DPRA=0;EPP=3.057;EPPR=3.0161;GTI=0;LEN=1;MEANALT=1;MQM=48.8401;MQMR=48.9326;NS=1;NUMALT=1;ODDS=1168.7;PAIRED=0.995968;PAIREDR=0.996438;PAO=0;PQA=0;PQR=0;PRO=0;QA=26185;QR=118988;RO=3369;RPL=355;RPP=6.38425;RPPR=98.548;RPR=389;RUN=1;SAF=375;SAP=3.11537;SAR=369;SRF=1695;SRP=3.29454;SRR=1674;TYPE=snp;ANN=T|stop_gained|HIGH|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.214A>T|p.Lys72*|214/366|214/366|72/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-149A>T|||||149|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-287A>T|||||287|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-667A>T|||||667|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1951A>T|||||1951|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2223A>T|||||2223|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1387A>T|||||1387|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1135A>T|||||1135|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*416A>T|||||416|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*220A>T|||||220|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4113:3369,744:3369:118988:744:26185:-910.007,0,-8604.41
NC_045512.2	27625	.	C	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=75;CIGAR=1X;DP=4049;DPB=4049;DPRA=0;EPP=3.03925;EPPR=4.91287;GTI=0;LEN=1;MEANALT=2;MQM=49.64;MQMR=49.5318;NS=1;NUMALT=1;ODDS=4751.09;PAIRED=1;PAIREDR=0.997231;PAO=0;PQA=0;PQR=0;PRO=0;QA=2649;QR=139228;RO=3973;RPL=31;RPP=7.90335;RPPR=56.556;RPR=44;RUN=1;SAF=37;SAP=3.03925;SAR=38;SRF=1999;SRP=3.3519;SRR=1974;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.232C>T|p.Arg78Cys|232/366|232/366|78/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-131C>T|||||131|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-269C>T|||||269|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-649C>T|||||649|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1933C>T|||||1933|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2241C>T|||||2241|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1405C>T|||||1405|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1153C>T|||||1153|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*434C>T|||||434|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*238C>T|||||238|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4049:3973,75:3973:139228:75:2649:0,-1000.05,-11370.5
NC_045512.2	27629	.	C	A	6085.31	.	AB=0.191634;ABP=3399.26;AC=1;AF=0.5;AN=2;AO=788;CIGAR=1X;DP=4112;DPB=4112;DPRA=0;EPP=3.18666;EPPR=6.31437;GTI=0;LEN=1;MEANALT=3;MQM=47.4569;MQMR=50.4522;NS=1;NUMALT=1;ODDS=1401.19;PAIRED=0.997462;PAIREDR=0.996378;PAO=0;PQA=0;PQR=0;PRO=0;QA=27332;QR=115748;RO=3313;RPL=348;RPP=26.3343;RPPR=44.9644;RPR=440;RUN=1;SAF=396;SAP=3.05439;SAR=392;SRF=1671;SRP=3.56152;SRR=1642;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.236C>A|p.Ala79Asp|236/366|236/366|79/121||,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-127C>A|||||127|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-265C>A|||||265|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-645C>A|||||645|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1929C>A|||||1929|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2245C>A|||||2245|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1409C>A|||||1409|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1157C>A|||||1157|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*438C>A|||||438|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*242C>A|||||242|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4112:3313,788:3313:115748:788:27332:-982.348,0,-8505.98
NC_045512.2	27638	.	T	C	53884.9	.	AB=0.555904;ABP=115.422;AC=1;AF=0.5;AN=2;AO=2302;CIGAR=1X;DP=4141;DPB=4141;DPRA=0;EPP=3.31593;EPPR=4.07359;GTI=0;LEN=1;MEANALT=2;MQM=48.9466;MQMR=52.1322;NS=1;NUMALT=1;ODDS=9722.66;PAIRED=0.996959;PAIREDR=0.996736;PAO=0;PQA=0;PQR=0;PRO=0;QA=80818;QR=63827;RO=1838;RPL=1086;RPP=18.952;RPPR=13.4494;RPR=1216;RUN=1;SAF=1166;SAP=3.85927;SAR=1136;SRF=930;SRP=3.58211;SRR=908;TYPE=snp;ANN=C|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.245T>C|p.Val82Ala|245/366|245/366|82/121||,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-118T>C|||||118|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-256T>C|||||256|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-636T>C|||||636|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1920T>C|||||1920|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2254T>C|||||2254|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1418T>C|||||1418|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1166T>C|||||1166|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*447T>C|||||447|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*251T>C|||||251|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4141:1838,2302:1838:63827:2302:80818:-5410.76,0,-4244.12
NC_045512.2	27652	.	T	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=46;CIGAR=1X;DP=4346;DPB=4346;DPRA=0;EPP=4.70971;EPPR=4.53826;GTI=0;LEN=1;MEANALT=2;MQM=46.5435;MQMR=50.996;NS=1;NUMALT=1;ODDS=5527.41;PAIRED=1;PAIREDR=0.996743;PAO=0;PQA=0;PQR=0;PRO=0;QA=1543;QR=149454;RO=4299;RPL=1;RPP=94.401;RPPR=11.1572;RPR=45;RUN=1;SAF=25;SAP=3.76559;SAR=21;SRF=2162;SRP=3.32599;SRR=2137;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.259T>A|p.Phe87Ile|259/366|259/366|87/121||,A|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-104T>A|||||104|,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-242T>A|||||242|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-622T>A|||||622|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1906T>A|||||1906|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2268T>A|||||2268|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1432T>A|||||1432|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1180T>A|||||1180|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*461T>A|||||461|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*265T>A|||||265|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4346:4299,46:4299:149454:46:1543:0,-1185.76,-12544.7
NC_045512.2	27696	.	T	C	9.00448E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=57;CIGAR=1X;DP=5194;DPB=5194;DPRA=0;EPP=3.0484;EPPR=3.68677;GTI=0;LEN=1;MEANALT=2;MQM=47.6491;MQMR=52.3927;NS=1;NUMALT=1;ODDS=6534.38;PAIRED=1;PAIREDR=0.985592;PAO=0;PQA=0;PQR=0;PRO=0;QA=1986;QR=181866;RO=5136;RPL=28;RPP=3.0484;RPPR=15.8108;RPR=29;RUN=1;SAF=28;SAP=3.0484;SAR=29;SRF=2583;SRP=3.39081;SRR=2553;TYPE=snp;ANN=C|synonymous_variant|LOW|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.303T>C|p.Phe101Phe|303/366|303/366|101/121||,C|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-60T>C|||||60|,C|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-198T>C|||||198|,C|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-578T>C|||||578|,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1862T>C|||||1862|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2312T>C|||||2312|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1476T>C|||||1476|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1224T>C|||||1224|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*505T>C|||||505|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*309T>C|||||309|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:5194:5136,57:5136:181866:57:1986:0,-1404.69,-15506.5
NC_045512.2	27752	.	C	T	65709.1	.	AB=0.548083;ABP=103.035;AC=1;AF=0.5;AN=2;AO=2730;CIGAR=1X;DP=4981;DPB=4981;DPRA=0;EPP=7.60459;EPPR=11.013;GTI=0;LEN=1;MEANALT=2;MQM=50.2674;MQMR=52.0516;NS=1;NUMALT=1;ODDS=12106.1;PAIRED=0.989377;PAIREDR=0.993769;PAO=0;PQA=0;PQR=0;PRO=0;QA=96766;QR=78943;RO=2247;RPL=1468;RPP=36.7644;RPPR=20.1047;RPR=1262;RUN=1;SAF=1333;SAP=6.2683;SAR=1397;SRF=1104;SRP=4.48018;SRR=1143;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding|1/1|c.359C>T|p.Thr120Ile|359/366|359/366|120/121||,T|upstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.-4C>T|||||4|,T|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-142C>T|||||142|,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-522C>T|||||522|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1806C>T|||||1806|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2368C>T|||||2368|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1532C>T|||||1532|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1280C>T|||||1280|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*561C>T|||||561|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*365C>T|||||365|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4981:2247,2730:2247:78943:2730:96766:-6594.66,0,-5279.74
NC_045512.2	27777	.	G	A	2.06367E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=4362;DPB=4362;DPRA=0;EPP=3.0103;EPPR=7.8761;GTI=0;LEN=1;MEANALT=2;MQM=46.5676;MQMR=51.2193;NS=1;NUMALT=1;ODDS=5211.88;PAIRED=1;PAIREDR=0.988567;PAO=0;PQA=0;PQR=0;PRO=0;QA=2614;QR=150803;RO=4286;RPL=49;RPP=19.9126;RPPR=772.005;RPR=25;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=2091;SRP=8.49015;SRR=2195;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.22G>A|p.Asp8Asn|22/132|22/132|8/43||,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-117G>A|||||117|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-497G>A|||||497|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1781G>A|||||1781|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2393G>A|||||2393|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1557G>A|||||1557|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1305G>A|||||1305|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*586G>A|||||586|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*390G>A|||||390|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*18G>A|||||18|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4362:4286,74:4286:150803:74:2614:0,-1105.72,-12659.9
NC_045512.2	27857	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=16;CIGAR=1X;DP=1159;DPB=1159;DPRA=0;EPP=3.0103;EPPR=3.05796;GTI=0;LEN=1;MEANALT=2;MQM=46.75;MQMR=48.8033;NS=1;NUMALT=1;ODDS=1424.16;PAIRED=1;PAIREDR=0.924495;PAO=0;PQA=0;PQR=0;PRO=0;QA=528;QR=39898;RO=1139;RPL=10;RPP=5.18177;RPPR=3.10372;RPR=6;RUN=1;SAF=8;SAP=3.0103;SAR=8;SRF=573;SRP=3.10372;SRR=566;TYPE=snp;ANN=A|synonymous_variant|LOW|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.102G>A|p.Leu34Leu|102/132|102/132|34/43||,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-37G>A|||||37|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-417G>A|||||417|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1701G>A|||||1701|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2473G>A|||||2473|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1637G>A|||||1637|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1385G>A|||||1385|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*666G>A|||||666|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*470G>A|||||470|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*98G>A|||||98|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1159:1139,16:1139:39898:16:528:0,-302.123,-3258.71
NC_045512.2	27864	.	C	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=66;CIGAR=1X;DP=1237;DPB=1237;DPRA=0;EPP=3.53672;EPPR=3.05674;GTI=0;LEN=1;MEANALT=2;MQM=43.9848;MQMR=49.7802;NS=1;NUMALT=1;ODDS=1098.27;PAIRED=0.984848;PAIREDR=0.939264;PAO=0;PQA=0;PQR=0;PRO=0;QA=2278;QR=40992;RO=1169;RPL=1;RPP=137.773;RPPR=9.04547;RPR=65;RUN=1;SAF=34;SAP=3.1419;SAR=32;SRF=587;SRP=3.05674;SRR=582;TYPE=snp;ANN=A|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.109C>A|p.His37Asn|109/132|109/132|37/43||,A|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-30C>A|||||30|,A|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-410C>A|||||410|,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1694C>A|||||1694|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2480C>A|||||2480|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1644C>A|||||1644|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1392C>A|||||1392|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*673C>A|||||673|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*477C>A|||||477|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*105C>A|||||105|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1237:1169,66:1169:40992:66:2278:0,-193.616,-3261.46
NC_045512.2	27870	.	GAAAC	TAAAT,TAAAC,GAAAT	28573.3	.	AB=0.0133648,0.0196541,0.855346;ABP=2619.44,2552.24,1398.11;AC=0,0,1;AF=0,0,0.5;AN=2;AO=17,25,1088;CIGAR=1X3M1X,1X4M,4M1X;DP=1272;DPB=1277;DPRA=0,0,0;EPP=3.13803,3.09716,3.52123;EPPR=3.26577;GTI=0;LEN=5,1,1;MEANALT=7,7,7;MQM=35.8824,37.32,50.6305;MQMR=52.1103;NS=1;NUMALT=3;ODDS=350.184;PAIRED=0.823529,0.76,0.983456;PAIREDR=0.941176;PAO=12.5,0.5,12;PQA=409,7,402;PQR=0;PRO=0;QA=597,665,38499;QR=4734;RO=136;RPL=1,0,534;RPP=31.7504,57.2971,3.80864;RPPR=3.26577;RPR=16,25,554;RUN=1,1,1;SAF=8,12,550;SAP=3.13803,3.09716,3.2977;SAR=9,13,538;SRF=70;SRP=3.26577;SRR=66;TYPE=complex,snp,snp;ANN=TAAAC|stop_gained|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.115G>T|p.Glu39*|115/132|115/132|39/43||,TAAAT|stop_gained|HIGH|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.115_119delGAAACinsTAAAT|p.GluThr39*|115/132|115/132|39/43||,GAAAT|missense_variant|MODERATE|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding|1/1|c.119C>T|p.Thr40Ile|119/132|119/132|40/43||,TAAAC|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-24G>T|||||24|,TAAAT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-24_-20delGAAACinsTAAAT|||||24|,GAAAT|upstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.-20C>T|||||20|,TAAAC|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-404G>T|||||404|,TAAAT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-404_-400delGAAACinsTAAAT|||||404|,GAAAT|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-400C>T|||||400|,TAAAC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1688G>T|||||1688|,TAAAT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1688_-1684delGAAACinsTAAAT|||||1688|,GAAAT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1684C>T|||||1684|,TAAAC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2486G>T|||||2486|,TAAAT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2486_*2490delGAAACinsTAAAT|||||2486|,GAAAT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2490C>T|||||2490|,TAAAC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1650G>T|||||1650|,TAAAT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1650_*1654delGAAACinsTAAAT|||||1650|,GAAAT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1654C>T|||||1654|,TAAAC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1398G>T|||||1398|,TAAAT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1398_*1402delGAAACinsTAAAT|||||1398|,GAAAT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1402C>T|||||1402|,TAAAC|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*679G>T|||||679|,TAAAT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*679_*683delGAAACinsTAAAT|||||679|,GAAAT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*683C>T|||||683|,TAAAC|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*483G>T|||||483|,TAAAT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*483_*487delGAAACinsTAAAT|||||483|,GAAAT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*487C>T|||||487|,TAAAC|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*111G>T|||||111|,TAAAT|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*111_*115delGAAACinsTAAAT|||||111|,GAAAT|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*115C>T|||||115|	GT:DP:AD:RO:QR:AO:QA:GL	0/3:1272:136,17,25,1088:136:4734:17,25,1088:597,665,38499:-2896.73,-2902.78,-3263.11,-2887.86,-3218.42,-3245.78,0,-330.591,-315.679,-37.9604
NC_045512.2	27942	.	C	T	0.0	.	AB=0.128987;ABP=1690.03;AC=1;AF=0.5;AN=2;AO=182;CIGAR=1X;DP=1411;DPB=1411;DPRA=0;EPP=3.05802;EPPR=4.49623;GTI=0;LEN=1;MEANALT=1;MQM=45.6429;MQMR=53.1587;NS=1;NUMALT=1;ODDS=303.191;PAIRED=0.983516;PAIREDR=0.981286;PAO=0;PQA=0;PQR=0;PRO=0;QA=6276;QR=43106;RO=1229;RPL=105;RPP=12.3643;RPPR=3.09688;RPR=77;RUN=1;SAF=89;SAP=3.2012;SAR=93;SRF=616;SRP=3.0262;SRR=613;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.49C>T|p.His17Tyr|49/366|49/366|17/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-332C>T|||||332|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1616C>T|||||1616|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2558C>T|||||2558|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1722C>T|||||1722|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1470C>T|||||1470|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*751C>T|||||751|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*555C>T|||||555|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*183C>T|||||183|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*55C>T|||||55|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1411:1229,182:1229:43106:182:6276:-65.6317,0,-3323.38
NC_045512.2	27972	.	C	T	7.85929E-14	.	AB=0.114679;ABP=1689.83;AC=1;AF=0.5;AN=2;AO=150;CIGAR=1X;DP=1308;DPB=1308;DPRA=0;EPP=3.0103;EPPR=3.37975;GTI=0;LEN=1;MEANALT=3;MQM=46.5933;MQMR=53.855;NS=1;NUMALT=1;ODDS=387.178;PAIRED=1;PAIREDR=0.987847;PAO=0;PQA=0;PQR=0;PRO=0;QA=5274;QR=39803;RO=1152;RPL=87;RPP=11.3488;RPPR=3.28173;RPR=63;RUN=1;SAF=74;SAP=3.06821;SAR=76;SRF=571;SRP=3.1988;SRR=581;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.79C>T|p.Gln27*|79/366|79/366|27/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-302C>T|||||302|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1586C>T|||||1586|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2588C>T|||||2588|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1752C>T|||||1752|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1500C>T|||||1500|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*781C>T|||||781|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*585C>T|||||585|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*213C>T|||||213|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*85C>T|||||85|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:1308:1152,150:1152:39803:150:5274:-29.6341,0,-3107.07
NC_045512.2	27981	.	CCA	CTACA	2.43493E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=15;CIGAR=1M2I2M;DP=1259;DPB=1269.33;DPRA=0;EPP=3.15506;EPPR=4.91888;GTI=0;LEN=2;MEANALT=4;MQM=47;MQMR=53.2139;NS=1;NUMALT=1;ODDS=1576.8;PAIRED=0.933333;PAIREDR=0.991929;PAO=0.5;PQA=0;PQR=0;PRO=0.5;QA=476;QR=43082;RO=1239;RPL=2;RPP=20.5268;RPPR=14.5091;RPR=13;RUN=1;SAF=7;SAP=3.15506;SAR=8;SRF=615;SRP=3.15226;SRR=624;TYPE=ins;ANN=CTACA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.88_89insTA|p.Pro30fs|89/366|89/366|30/121||,CTACA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-293_-292insTA|||||292|,CTACA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1577_-1576insTA|||||1576|,CTACA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2597_*2598insTA|||||2598|,CTACA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1761_*1762insTA|||||1762|,CTACA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1509_*1510insTA|||||1510|,CTACA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*790_*791insTA|||||791|,CTACA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*594_*595insTA|||||595|,CTACA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*222_*223insTA|||||223|,CTACA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*94_*95insTA|||||95|;LOF=(ORF8|GU280_gp09|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1259:1239,15:1239:43082:15:476:0,-335.717,-3717.41
NC_045512.2	27987	.	GTAG	GG	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=17;CIGAR=1M2D1M;DP=1259;DPB=1250.5;DPRA=0;EPP=3.13803;EPPR=3.35409;GTI=0;LEN=2;MEANALT=3;MQM=48.1176;MQMR=53.3328;NS=1;NUMALT=1;ODDS=1571.36;PAIRED=0.941176;PAIREDR=0.991115;PAO=0;PQA=0;PQR=0;PRO=0;QA=486;QR=43228;RO=1238;RPL=2;RPP=24.5973;RPPR=31.7481;RPR=15;RUN=1;SAF=8;SAP=3.13803;SAR=9;SRF=609;SRP=3.71191;SRR=629;TYPE=del;ANN=GG|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.95_96delTA|p.Val32fs|95/366|95/366|32/121||,GG|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-286_-285delTA|||||286|,GG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1570_-1569delTA|||||1570|,GG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2604_*2605delTA|||||2604|,GG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1768_*1769delTA|||||1768|,GG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1516_*1517delTA|||||1516|,GG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*797_*798delTA|||||797|,GG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*601_*602delTA|||||601|,GG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*229_*230delTA|||||229|,GG|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*101_*102delTA|||||101|;LOF=(ORF8|GU280_gp09|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1259:1238,17:1238:43228:17:486:0,-336.27,-3738.37
NC_045512.2	28048	.	G	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=133;CIGAR=1X;DP=1234;DPB=1234;DPRA=0;EPP=3.15724;EPPR=3.24894;GTI=0;LEN=1;MEANALT=1;MQM=42.4511;MQMR=52.6803;NS=1;NUMALT=1;ODDS=498.144;PAIRED=1;PAIREDR=0.993642;PAO=0;PQA=0;PQR=0;PRO=0;QA=4623;QR=38646;RO=1101;RPL=56;RPP=10.2104;RPPR=15.3193;RPR=77;RUN=1;SAF=65;SAP=3.15724;SAR=68;SRF=528;SRP=7.00415;SRR=573;TYPE=snp;ANN=T|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.155G>T|p.Arg52Ile|155/366|155/366|52/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-226G>T|||||226|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1510G>T|||||1510|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2664G>T|||||2664|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1828G>T|||||1828|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1576G>T|||||1576|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*857G>T|||||857|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*661G>T|||||661|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*289G>T|||||289|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*161G>T|||||161|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:1234:1101,133:1101:38646:133:4623:0,-20.4073,-2999.34
NC_045512.2	28095	.	A	T	1.91419E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=95;CIGAR=1X;DP=2258;DPB=2258;DPRA=0;EPP=3.03316;EPPR=31.6832;GTI=0;LEN=1;MEANALT=1;MQM=36.3368;MQMR=50.2603;NS=1;NUMALT=1;ODDS=2252.59;PAIRED=1;PAIREDR=0.992141;PAO=0;PQA=0;PQR=0;PRO=0;QA=3257;QR=76414;RO=2163;RPL=75;RPP=72.1546;RPPR=1509.51;RPR=20;RUN=1;SAF=46;SAP=3.21602;SAR=49;SRF=1157;SRP=25.9006;SRR=1006;TYPE=snp;ANN=T|stop_gained|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.202A>T|p.Lys68*|202/366|202/366|68/121||,T|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-179A>T|||||179|,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1463A>T|||||1463|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2711A>T|||||2711|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1875A>T|||||1875|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1623A>T|||||1623|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*904A>T|||||904|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*708A>T|||||708|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*336A>T|||||336|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*208A>T|||||208|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2258:2163,95:2163:76414:95:3257:0,-455.717,-6188.95
NC_045512.2	28111	.	A	G	30254.2	.	AB=0.521647;ABP=14.5739;AC=1;AF=0.5;AN=2;AO=1482;CIGAR=1X;DP=2841;DPB=2841;DPRA=0;EPP=22.0524;EPPR=10.6289;GTI=0;LEN=1;MEANALT=2;MQM=47.7821;MQMR=51.2771;NS=1;NUMALT=1;ODDS=6966.29;PAIRED=0.992578;PAIREDR=0.992631;PAO=0;PQA=0;PQR=0;PRO=0;QA=51828;QR=48256;RO=1357;RPL=66;RPP=2673.39;RPPR=281.268;RPR=1416;RUN=1;SAF=796;SAP=20.7396;SAR=686;SRF=701;SRP=6.25071;SRR=656;TYPE=snp;ANN=G|missense_variant|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.218A>G|p.Tyr73Cys|218/366|218/366|73/121||,G|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-163A>G|||||163|,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1447A>G|||||1447|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2727A>G|||||2727|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*1891A>G|||||1891|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1639A>G|||||1639|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*920A>G|||||920|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*724A>G|||||724|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*352A>G|||||352|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*224A>G|||||224|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2841:1357,1482:1357:48256:1482:51828:-3367.71,0,-3253.93
NC_045512.2	28242	.	GTTTTAGATTTCA	GTTTTAA,GTTTTTAGATTTCA	21929.6	.	AB=0.252466,0.0809736;ABP=3348.5,9589.76;AC=1,0;AF=0.5,0;AN=2;AO=1587,509;CIGAR=6M6D1M,1M1I12M;DP=6286;DPB=5604.62;DPRA=0,0;EPP=3.40574,3.11695;EPPR=3.2873;GTI=0;LEN=6,1;MEANALT=21,21;MQM=47.1979,46.4597;MQMR=50.1179;NS=1;NUMALT=2;ODDS=5049.48;PAIRED=0.993699,0.994106;PAIREDR=0.99156;PAO=18.6667,39.1667;PQA=641,1351;PQR=1351;PRO=39.1667;QA=52030,16119;QR=145691;RO=4147;RPL=901,310;RPP=66.2594,55.5736;RPPR=51.0838;RPR=686,199;RUN=1,1;SAF=786,251;SAP=3.31816,3.21934;SAR=801,258;SRF=2052;SRP=3.97848;SRR=2095;TYPE=del,ins;ANN=GTTTTTAGATTTCA|frameshift_variant|HIGH|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.353dupT|p.Leu118fs|354/366|354/366|118/121||,GTTTTAA|conservative_inframe_deletion|MODERATE|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding|1/1|c.355_360delGATTTC|p.Asp119_Phe120del|355/366|355/366|119/121||,GTTTTTAGATTTCA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-28dupT|||||27|,GTTTTAA|upstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.-26_-21delGATTTC|||||26|,GTTTTTAGATTTCA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1312dupT|||||1311|,GTTTTAA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1310_-1305delGATTTC|||||1310|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2862dupT|||||2863|,GTTTTAA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2864_*2869delGATTTC|||||2864|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2026dupT|||||2027|,GTTTTAA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2028_*2033delGATTTC|||||2028|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1774dupT|||||1775|,GTTTTAA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1776_*1781delGATTTC|||||1776|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1055dupT|||||1056|,GTTTTAA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1057_*1062delGATTTC|||||1057|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*859dupT|||||860|,GTTTTAA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*861_*866delGATTTC|||||861|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*487dupT|||||488|,GTTTTAA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*489_*494delGATTTC|||||489|,GTTTTTAGATTTCA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*359dupT|||||360|,GTTTTAA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*361_*366delGATTTC|||||361|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6286:4147,1587,509:4147:145691:1587,509:52030,16119:-2465.57,0,-10582,-2450.21,-9796.04,-13356.8
NC_045512.2	28270	.	TAAAATG	TAAATG	162166.0	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6075;CIGAR=1M1D5M;DP=6091;DPB=5242.14;DPRA=0;EPP=3.02781;EPPR=0;GTI=0;LEN=1;MEANALT=13;MQM=46.504;MQMR=0;NS=1;NUMALT=1;ODDS=8426.34;PAIRED=0.985021;PAIREDR=0;PAO=62.5;PQA=2061.5;PQR=2085.5;PRO=63.5;QA=184797;QR=0;RO=0;RPL=2885;RPP=36.2615;RPPR=0;RPR=3190;RUN=1;SAF=3053;SAP=3.3538;SAR=3022;SRF=0;SRP=0;SRR=0;TYPE=del;ANN=TAAATG|frameshift_variant&start_lost|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1delA|p.Met1fs|1/1260|1/1260|1/419||INFO_REALIGN_3_PRIME,TAAATG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1284delA|||||1284|,TAAATG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2890delA|||||2890|,TAAATG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2054delA|||||2054|,TAAATG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1802delA|||||1802|,TAAATG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1083delA|||||1083|,TAAATG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*887delA|||||887|,TAAATG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*515delA|||||515|,TAAATG|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*387delA|||||387|,TAAATG|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*15delA|||||15|;LOF=(N|GU280_gp10|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	1/1:6091:0,6075:0:0:6075:184797:-16226,-1828.76,0
NC_045512.2	28280	.	GAT	CTA	78730.3	.	AB=0.542129;ABP=100.346;AC=1;AF=0.5;AN=2;AO=3423;CIGAR=3X;DP=6314;DPB=6358.67;DPRA=0;EPP=4.66031;EPPR=4.82376;GTI=0;LEN=3;MEANALT=9;MQM=47.7812;MQMR=44.7071;NS=1;NUMALT=1;ODDS=13474;PAIRED=0.991528;PAIREDR=0.969739;PAO=134;PQA=4677;PQR=0;PRO=0;QA=120731;QR=100878;RO=2875;RPL=2093;RPP=372.325;RPPR=363.649;RPR=1330;RUN=1;SAF=1701;SAP=3.29006;SAR=1722;SRF=1446;SRP=3.22858;SRR=1429;TYPE=mnp;ANN=CTA|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.7_9delGATinsCTA|p.Asp3Leu|7/1260|7/1260|3/419||,CTA|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1278_-1276delGATinsCTA|||||1278|,CTA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2896_*2898delGATinsCTA|||||2896|,CTA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2060_*2062delGATinsCTA|||||2060|,CTA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1808_*1810delGATinsCTA|||||1808|,CTA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1089_*1091delGATinsCTA|||||1089|,CTA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*893_*895delGATinsCTA|||||893|,CTA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*521_*523delGATinsCTA|||||521|,CTA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*393_*395delGATinsCTA|||||393|,CTA|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*21_*23delGATinsCTA|||||21|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:6314:2875,3423:2875:100878:3423:120731:-7930.42,0,-5908.15
NC_045512.2	28295	.	A	G	1.00676E-12	.	AB=0.129612;ABP=9012.63;AC=1;AF=0.5;AN=2;AO=980;CIGAR=1X;DP=7561;DPB=7561;DPRA=0;EPP=3.23188;EPPR=3.26911;GTI=0;LEN=1;MEANALT=3;MQM=45.3653;MQMR=46.2847;NS=1;NUMALT=1;ODDS=1467.02;PAIRED=0.945918;PAIREDR=0.96017;PAO=0;PQA=0;PQR=0;PRO=0;QA=34084;QR=230830;RO=6578;RPL=539;RPP=24.2907;RPPR=6.58078;RPR=441;RUN=1;SAF=482;SAP=3.57754;SAR=498;SRF=3262;SRP=3.9729;SRR=3316;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.22A>G|p.Asn8Asp|22/1260|22/1260|8/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1263A>G|||||1263|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*2911A>G|||||2911|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2075A>G|||||2075|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1823A>G|||||1823|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1104A>G|||||1104|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*908A>G|||||908|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*536A>G|||||536|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*408A>G|||||408|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*36A>G|||||36|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:7561:6578,980:6578:230830:980:34084:-382.745,0,-16005.3
NC_045512.2	28461	.	A	G	15382.4	.	AB=0.361009;ABP=368.81;AC=1;AF=0.5;AN=2;AO=787;CIGAR=1X;DP=2180;DPB=2180;DPRA=0;EPP=4.00636;EPPR=32.7183;GTI=0;LEN=1;MEANALT=2;MQM=48.2071;MQMR=50.8757;NS=1;NUMALT=1;ODDS=3541.92;PAIRED=0.986023;PAIREDR=0.984914;PAO=0;PQA=0;PQR=0;PRO=0;QA=27472;QR=45714;RO=1392;RPL=252;RPP=223.99;RPPR=356.461;RPR=535;RUN=1;SAF=405;SAP=4.4699;SAR=382;SRF=637;SRP=24.7313;SRR=755;TYPE=snp;ANN=G|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.188A>G|p.Asp63Gly|188/1260|188/1260|63/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-1097A>G|||||1097|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3077A>G|||||3077|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2241A>G|||||2241|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*1989A>G|||||1989|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1270A>G|||||1270|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1074A>G|||||1074|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*702A>G|||||702|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*574A>G|||||574|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*202A>G|||||202|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:2180:1392,787:1392:45714:787:27472:-1606.4,0,-3204.04
NC_045512.2	28567	.	C	T	4.22129E-16	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=26;CIGAR=1X;DP=2372;DPB=2372;DPRA=0;EPP=3.0103;EPPR=4.08121;GTI=0;LEN=1;MEANALT=2;MQM=50.0769;MQMR=52.7534;NS=1;NUMALT=1;ODDS=2985.45;PAIRED=1;PAIREDR=0.995307;PAO=0;PQA=0;PQR=0;PRO=0;QA=906;QR=81075;RO=2344;RPL=4;RPP=30.0702;RPPR=35.7528;RPR=22;RUN=1;SAF=13;SAP=3.0103;SAR=13;SRF=1173;SRP=3.01401;SRR=1171;TYPE=snp;ANN=T|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.294C>T|p.Asp98Asp|294/1260|294/1260|98/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-991C>T|||||991|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3183C>T|||||3183|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2347C>T|||||2347|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2095C>T|||||2095|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1376C>T|||||1376|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1180C>T|||||1180|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*808C>T|||||808|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*680C>T|||||680|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*308C>T|||||308|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2372:2344,26:2344:81075:26:906:0,-636.928,-6974.26
NC_045512.2	28579	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=86;CIGAR=1X;DP=2340;DPB=2340;DPRA=0;EPP=3.1113;EPPR=5.22994;GTI=0;LEN=1;MEANALT=1;MQM=48.9651;MQMR=52.7955;NS=1;NUMALT=1;ODDS=2324.18;PAIRED=1;PAIREDR=0.996894;PAO=0;PQA=0;PQR=0;PRO=0;QA=2951;QR=78442;RO=2254;RPL=40;RPP=3.91929;RPPR=39.2683;RPR=46;RUN=1;SAF=42;SAP=3.1113;SAR=44;SRF=1099;SRP=6.03148;SRR=1155;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.306A>T|p.Lys102Asn|306/1260|306/1260|102/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-979A>T|||||979|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3195A>T|||||3195|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2359A>T|||||2359|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2107A>T|||||2107|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1388A>T|||||1388|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1192A>T|||||1192|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*820A>T|||||820|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*692A>T|||||692|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*320A>T|||||320|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2340:2254,86:2254:78442:86:2951:0,-458.341,-6586.23
NC_045512.2	28598	.	T	C	2.20595E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=27;CIGAR=1X;DP=2328;DPB=2328;DPRA=0;EPP=3.09072;EPPR=3.05658;GTI=0;LEN=1;MEANALT=2;MQM=46.5185;MQMR=52.5028;NS=1;NUMALT=1;ODDS=2914.06;PAIRED=1;PAIREDR=0.996085;PAO=0;PQA=0;PQR=0;PRO=0;QA=942;QR=80683;RO=2299;RPL=16;RPP=5.02092;RPPR=42.7041;RPR=11;RUN=1;SAF=13;SAP=3.09072;SAR=14;SRF=1156;SRP=3.16993;SRR=1143;TYPE=snp;ANN=C|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.325T>C|p.Tyr109His|325/1260|325/1260|109/419||,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-960T>C|||||960|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3214T>C|||||3214|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2378T>C|||||2378|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2126T>C|||||2126|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1407T>C|||||1407|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1211T>C|||||1211|,C|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*839T>C|||||839|,C|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*711T>C|||||711|,C|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*339T>C|||||339|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2328:2299,27:2299:80683:27:942:0,-623.497,-6905.87
NC_045512.2	28881	.	GGGG	AACC,AACG,TGGG	91355.5	.	AB=0.0998312,0.256089,0.638775;ABP=5771.14,2145.96,696.709;AC=0,1,1;AF=0,0.5,0.5;AN=2;AO=414,1062,2649;CIGAR=4X,3X1M,1X3M;DP=4147;DPB=4199.25;DPRA=0,0,0;EPP=3.03128,3.08391,3.30622;EPPR=5.18177;GTI=0;LEN=4,3,1;MEANALT=14,14,14;MQM=48.314,48.1742,48.4179;MQMR=60;NS=1;NUMALT=3;ODDS=3919.48;PAIRED=1,0.997175,1;PAIREDR=1;PAO=10.5,2.5,101;PQA=343,88,3369;PQR=1079;PRO=62;QA=14330,33717,84424;QR=21;RO=1;RPL=203,506,1423;RPP=3.34599,8.12205,34.8233;RPPR=5.18177;RPR=211,556,1226;RUN=1,1,1;SAF=207,534,1330;SAP=3.0103,3.08391,3.10949;SAR=207,528,1319;SRF=0;SRP=5.18177;SRR=1;TYPE=complex,mnp,snp;ANN=TGGG|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608G>T|p.Arg203Met|608/1260|608/1260|203/419||,AACG|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608_610delGGGinsAAC|p.ArgGly203LysArg|608/1260|608/1260|203/419||,AACC|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.608_611delGGGGinsAACC|p.ArgGly203LysPro|608/1260|608/1260|203/419||,TGGG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-677G>T|||||677|,AACG|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-677_-675delGGGinsAAC|||||677|,AACC|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-677_-674delGGGGinsAACC|||||677|,TGGG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3497G>T|||||3497|,AACG|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3497_*3499delGGGinsAAC|||||3497|,AACC|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3497_*3500delGGGGinsAACC|||||3497|,TGGG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2661G>T|||||2661|,AACG|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2661_*2663delGGGinsAAC|||||2661|,AACC|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2661_*2664delGGGGinsAACC|||||2661|,TGGG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2409G>T|||||2409|,AACG|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2409_*2411delGGGinsAAC|||||2409|,AACC|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2409_*2412delGGGGinsAACC|||||2409|,TGGG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1690G>T|||||1690|,AACG|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1690_*1692delGGGinsAAC|||||1690|,AACC|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1690_*1693delGGGGinsAACC|||||1690|,TGGG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1494G>T|||||1494|,AACG|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1494_*1496delGGGinsAAC|||||1494|,AACC|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1494_*1497delGGGGinsAACC|||||1494|,TGGG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1122G>T|||||1122|,AACG|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1122_*1124delGGGinsAAC|||||1122|,AACC|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1122_*1125delGGGGinsAACC|||||1122|,TGGG|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*994G>T|||||994|,AACG|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*994_*996delGGGinsAAC|||||994|,AACC|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*994_*997delGGGGinsAACC|||||994|,TGGG|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*622G>T|||||622|,AACG|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*622_*624delGGGinsAAC|||||622|,AACC|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*622_*625delGGGGinsAACC|||||622|	GT:DP:AD:RO:QR:AO:QA:GL	2/3:4147:1,414,1062,2649:1:21:414,1062,2649:14330,33717,84424:-9304.73,-8260.38,-8137.34,-6643.97,-5600.91,-6325.87,-2659.48,-1616.42,0,-1863.64
NC_045512.2	28915	.	CG	TT,CT	52376.7	.	AB=0.0279205,0.547018;ABP=8669.27,88.9772;AC=0,1;AF=0,0.5;AN=2;AO=125,2449;CIGAR=2X,1M1X;DP=4477;DPB=4484;DPRA=0,0;EPP=3.16665,3.56447;EPPR=3.56579;GTI=0;LEN=2,1;MEANALT=7,7;MQM=44.744,46.5545;MQMR=49.2706;NS=1;NUMALT=2;ODDS=9522.4;PAIRED=1,0.998367;PAIREDR=0.996829;PAO=8,6;PQA=264,196;PQR=0;PRO=0;QA=4248,82127;QR=65723;RO=1892;RPL=62,1210;RPP=3.02767,3.756;RPPR=8.96004;RPR=63,1239;RUN=1,1;SAF=64,1220;SAP=3.16665,3.08212;SAR=61,1229;SRF=929;SRP=4.33706;SRR=963;TYPE=mnp,snp;ANN=CT|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.643G>T|p.Gly215Cys|643/1260|643/1260|215/419||,TT|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.642_643delCGinsTT|p.Gly215Cys|642/1260|642/1260|214/419||,TT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-643_-642delCGinsTT|||||643|,CT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-642G>T|||||642|,TT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3531_*3532delCGinsTT|||||3531|,CT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3532G>T|||||3532|,TT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2695_*2696delCGinsTT|||||2695|,CT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2696G>T|||||2696|,TT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2443_*2444delCGinsTT|||||2443|,CT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2444G>T|||||2444|,TT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1724_*1725delCGinsTT|||||1724|,CT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1725G>T|||||1725|,TT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1528_*1529delCGinsTT|||||1528|,CT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1529G>T|||||1529|,TT|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1156_*1157delCGinsTT|||||1156|,CT|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1157G>T|||||1157|,TT|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1028_*1029delCGinsTT|||||1028|,CT|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1029G>T|||||1029|,TT|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*656_*657delCGinsTT|||||656|,CT|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*657G>T|||||657|	GT:DP:AD:RO:QR:AO:QA:GL	0/2:4477:1892,125,2449:1892:65723:125,2449:4248,82127:-5262.66,-5540.44,-10401,0,-4606.45,-4161
NC_045512.2	28972	.	A	G	5.40026E-14	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=108;CIGAR=1X;DP=4047;DPB=4047;DPRA=0;EPP=3.0103;EPPR=5.63492;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=46.8825;NS=1;NUMALT=1;ODDS=4445.98;PAIRED=0.981481;PAIREDR=0.995684;PAO=0;PQA=0;PQR=0;PRO=0;QA=3804;QR=138740;RO=3939;RPL=56;RPP=3.332;RPPR=289.586;RPR=52;RUN=1;SAF=52;SAP=3.332;SAR=56;SRF=1921;SRP=8.19725;SRR=2018;TYPE=snp;ANN=G|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.699A>G|p.Lys233Lys|699/1260|699/1260|233/419||,G|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-586A>G|||||586|,G|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3588A>G|||||3588|,G|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2752A>G|||||2752|,G|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2500A>G|||||2500|,G|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1781A>G|||||1781|,G|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1585A>G|||||1585|,G|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1213A>G|||||1213|,G|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1085A>G|||||1085|,G|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*713A>G|||||713|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:4047:3939,108:3939:138740:108:3804:0,-922.009,-10833.9
NC_045512.2	28977	.	C	T	25897.3	.	AB=0.383986;ABP=459.997;AC=1;AF=0.5;AN=2;AO=1501;CIGAR=1X;DP=3909;DPB=3909;DPRA=0;EPP=3.91448;EPPR=5.26474;GTI=0;LEN=1;MEANALT=1;MQM=41.2438;MQMR=50.309;NS=1;NUMALT=1;ODDS=5963.07;PAIRED=0.997335;PAIREDR=0.995432;PAO=0;PQA=0;PQR=0;PRO=0;QA=52393;QR=84353;RO=2408;RPL=949;RPP=231.021;RPPR=135.982;RPR=552;RUN=1;SAF=735;SAP=4.40056;SAR=766;SRF=1191;SRP=3.6199;SRR=1217;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.704C>T|p.Ser235Phe|704/1260|704/1260|235/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-581C>T|||||581|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3593C>T|||||3593|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2757C>T|||||2757|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2505C>T|||||2505|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1786C>T|||||1786|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1590C>T|||||1590|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1218C>T|||||1218|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1090C>T|||||1090|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*718C>T|||||718|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3909:2408,1501:2408:84353:1501:52393:-2668.08,0,-5930.49
NC_045512.2	29000	.	G	T	2875.6	.	AB=0.194681;ABP=3047.47;AC=1;AF=0.5;AN=2;AO=732;CIGAR=1X;DP=3760;DPB=3760;DPRA=0;EPP=3.97144;EPPR=12.9956;GTI=0;LEN=1;MEANALT=1;MQM=36.9194;MQMR=48.4699;NS=1;NUMALT=1;ODDS=662.131;PAIRED=0.998634;PAIREDR=0.988771;PAO=0;PQA=0;PQR=0;PRO=0;QA=25394;QR=104500;RO=3028;RPL=449;RPP=84.755;RPPR=22.7716;RPR=283;RUN=1;SAF=356;SAP=4.1969;SAR=376;SRF=1504;SRP=3.29715;SRR=1524;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.727G>T|p.Gly243Cys|727/1260|727/1260|243/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-558G>T|||||558|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3616G>T|||||3616|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2780G>T|||||2780|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2528G>T|||||2528|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1809G>T|||||1809|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1613G>T|||||1613|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1241G>T|||||1241|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1113G>T|||||1113|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*741G>T|||||741|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:3760:3028,732:3028:104500:732:25394:-631.313,0,-7432.98
NC_045512.2	29029	.	T	C	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=74;CIGAR=1X;DP=3572;DPB=3572;DPRA=0;EPP=3.47981;EPPR=17.1686;GTI=0;LEN=1;MEANALT=2;MQM=38.5541;MQMR=46.4673;NS=1;NUMALT=1;ODDS=4202.1;PAIRED=0.986486;PAIREDR=0.985702;PAO=0;PQA=0;PQR=0;PRO=0;QA=2455;QR=120356;RO=3497;RPL=47;RPP=14.748;RPPR=272.678;RPR=27;RUN=1;SAF=36;SAP=3.12768;SAR=38;SRF=1756;SRP=3.15001;SRR=1741;TYPE=snp;ANN=C|synonymous_variant|LOW|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.756T>C|p.Ala252Ala|756/1260|756/1260|252/419||,C|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-529T>C|||||529|,C|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3645T>C|||||3645|,C|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2809T>C|||||2809|,C|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2557T>C|||||2557|,C|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1838T>C|||||1838|,C|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1642T>C|||||1642|,C|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1270T>C|||||1270|,C|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1142T>C|||||1142|,C|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*770T>C|||||770|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3572:3497,74:3497:120356:74:2455:0,-898.696,-9450.46
NC_045512.2	29039	.	A	T	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=149;CIGAR=1X;DP=3516;DPB=3516;DPRA=0;EPP=4.77371;EPPR=20.1454;GTI=0;LEN=1;MEANALT=1;MQM=37.7181;MQMR=47.6341;NS=1;NUMALT=1;ODDS=3473.2;PAIRED=0.973154;PAIREDR=0.985744;PAO=0;PQA=0;PQR=0;PRO=0;QA=5164;QR=118588;RO=3367;RPL=86;RPP=10.7198;RPPR=174.061;RPR=63;RUN=1;SAF=76;SAP=3.14146;SAR=73;SRF=1658;SRP=4.68776;SRR=1709;TYPE=snp;ANN=T|stop_gained|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.766A>T|p.Lys256*|766/1260|766/1260|256/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-519A>T|||||519|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3655A>T|||||3655|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2819A>T|||||2819|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2567A>T|||||2567|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1848A>T|||||1848|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1652A>T|||||1652|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1280A>T|||||1280|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1152A>T|||||1152|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*780A>T|||||780|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3516:3367,149:3367:118588:149:5164:0,-709.856,-9327.62
NC_045512.2	29049	.	G	A	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=101;CIGAR=1X;DP=3347;DPB=3347;DPRA=0;EPP=6.64375;EPPR=12.4923;GTI=0;LEN=1;MEANALT=2;MQM=43.099;MQMR=49.1378;NS=1;NUMALT=1;ODDS=3614.81;PAIRED=0.960396;PAIREDR=0.990133;PAO=0;PQA=0;PQR=0;PRO=0;QA=3321;QR=110630;RO=3243;RPL=47;RPP=4.06379;RPPR=70.2965;RPR=54;RUN=1;SAF=48;SAP=3.54779;SAR=53;SRF=1609;SRP=3.42879;SRR=1634;TYPE=snp;ANN=A|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.776G>A|p.Arg259Gln|776/1260|776/1260|259/419||,A|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-509G>A|||||509|,A|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3665G>A|||||3665|,A|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2829G>A|||||2829|,A|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2577G>A|||||2577|,A|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1858G>A|||||1858|,A|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1662G>A|||||1662|,A|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1290G>A|||||1290|,A|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1162G>A|||||1162|,A|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*790G>A|||||790|	GT:DP:AD:RO:QR:AO:QA:GL	0/0:3347:3243,101:3243:110630:101:3321:0,-752.738,-8988.5
NC_045512.2	29067	.	CTAAAGCATACAATGT	CT	2.70012E-13	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=187;CIGAR=1M14D1M;DP=2118;DPB=1955.62;DPRA=0;EPP=3.02191;EPPR=5.31131;GTI=0;LEN=14;MEANALT=13;MQM=48.7647;MQMR=53.2214;NS=1;NUMALT=1;ODDS=1275.56;PAIRED=0.97861;PAIREDR=0.993197;PAO=1;PQA=34;PQR=101;PRO=3;QA=5285;QR=66815;RO=1911;RPL=76;RPP=17.2352;RPPR=87.6977;RPR=111;RUN=1;SAF=98;SAP=3.95088;SAR=89;SRF=986;SRP=7.23848;SRR=925;TYPE=del;ANN=CT|frameshift_variant|HIGH|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.798_811delAGCATACAATGTAA|p.Lys266fs|798/1260|798/1260|266/419||INFO_REALIGN_3_PRIME,CT|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-489_-476delAAAGCATACAATGT|||||489|,CT|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*3685_*3698delAAAGCATACAATGT|||||3685|,CT|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*2849_*2862delAAAGCATACAATGT|||||2849|,CT|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2597_*2610delAAAGCATACAATGT|||||2597|,CT|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*1878_*1891delAAAGCATACAATGT|||||1878|,CT|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*1682_*1695delAAAGCATACAATGT|||||1682|,CT|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1310_*1323delAAAGCATACAATGT|||||1310|,CT|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1182_*1195delAAAGCATACAATGT|||||1182|,CT|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*810_*823delAAAGCATACAATGT|||||810|;LOF=(N|GU280_gp10|1|1.00)	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2118:1911,187:1911:66815:187:5285:0,-187.495,-5392.39
NC_045512.2	29402	.	G	T	33928.1	.	AB=0.380005;ABP=537.172;AC=1;AF=0.5;AN=2;AO=1623;CIGAR=1X;DP=4271;DPB=4271;DPRA=0;EPP=4.13551;EPPR=7.75762;GTI=0;LEN=1;MEANALT=3;MQM=49.4449;MQMR=52.7301;NS=1;NUMALT=1;ODDS=7812.23;PAIRED=0.997535;PAIREDR=0.995079;PAO=0;PQA=0;PQR=0;PRO=0;QA=57174;QR=92750;RO=2642;RPL=779;RPP=8.66309;RPPR=18.6627;RPR=844;RUN=1;SAF=832;SAP=5.25937;SAR=791;SRF=1339;SRP=4.07549;SRR=1303;TYPE=snp;ANN=T|missense_variant|MODERATE|N|GU280_gp10|transcript|GU280_gp10|protein_coding|1/1|c.1129G>T|p.Asp377Tyr|1129/1260|1129/1260|377/419||,T|upstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.-156G>T|||||156|,T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4018G>T|||||4018|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*3182G>T|||||3182|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*2930G>T|||||2930|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*2211G>T|||||2211|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*2015G>T|||||2015|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1643G>T|||||1643|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1515G>T|||||1515|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*1143G>T|||||1143|	GT:DP:AD:RO:QR:AO:QA:GL	0/1:4271:2642,1623:2642:92750:1623:57174:-3456.1,0,-6754.07
NC_045512.2	29681	.	TTAATCA	TTAATCTAATCA	0.0	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=59;CIGAR=1M5I6M;DP=2108;DPB=2151.14;DPRA=0;EPP=3.34154;EPPR=24.183;GTI=0;LEN=5;MEANALT=6;MQM=52.322;MQMR=51.6699;NS=1;NUMALT=1;ODDS=2266.18;PAIRED=1;PAIREDR=0.995586;PAO=1;PQA=27.5;PQR=27.5;PRO=1;QA=1893;QR=70994;RO=2039;RPL=34;RPP=5.99147;RPPR=724.345;RPR=25;RUN=1;SAF=31;SAP=3.34154;SAR=28;SRF=963;SRP=16.6089;SRR=1076;TYPE=ins;ANN=TTAATCTAATCA|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4302_*4303insTAATC|||||4303|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*3466_*3467insTAATC|||||3467|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*3214_*3215insTAATC|||||3215|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*2495_*2496insTAATC|||||2496|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*2299_*2300insTAATC|||||2300|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1927_*1928insTAATC|||||1928|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1799_*1800insTAATC|||||1800|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*1427_*1428insTAATC|||||1428|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.*153_*154insTAATC|||||154|,TTAATCTAATCA|downstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.*12_*13insTAATC|||||13|,TTAATCTAATCA|intergenic_region|MODIFIER|ORF10-CHR_END|GU280_gp11-CHR_END|intergenic_region|GU280_gp11-CHR_END|||n.29686_29687insTAATC||||||	GT:DP:AD:RO:QR:AO:QA:GL	0/0:2108:2039,59:2039:70994:59:1893:0,-462.802,-5912.21
NC_045512.2	29742	.	G	T	36691.9	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=1276;CIGAR=1X;DP=1276;DPB=1276;DPRA=0;EPP=3.69101;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=49.6567;MQMR=0;NS=1;NUMALT=1;ODDS=1773.52;PAIRED=0.996082;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=44133;QR=0;RO=0;RPL=591;RPP=18.0472;RPPR=0;RPR=685;RUN=1;SAF=637;SAP=3.01711;SAR=639;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|downstream_gene_variant|MODIFIER|S|GU280_gp02|transcript|GU280_gp02|protein_coding||c.*4358G>T|||||4358|,T|downstream_gene_variant|MODIFIER|ORF3a|GU280_gp03|transcript|GU280_gp03|protein_coding||c.*3522G>T|||||3522|,T|downstream_gene_variant|MODIFIER|E|GU280_gp04|transcript|GU280_gp04|protein_coding||c.*3270G>T|||||3270|,T|downstream_gene_variant|MODIFIER|M|GU280_gp05|transcript|GU280_gp05|protein_coding||c.*2551G>T|||||2551|,T|downstream_gene_variant|MODIFIER|ORF6|GU280_gp06|transcript|GU280_gp06|protein_coding||c.*2355G>T|||||2355|,T|downstream_gene_variant|MODIFIER|ORF7a|GU280_gp07|transcript|GU280_gp07|protein_coding||c.*1983G>T|||||1983|,T|downstream_gene_variant|MODIFIER|ORF7b|GU280_gp08|transcript|GU280_gp08|protein_coding||c.*1855G>T|||||1855|,T|downstream_gene_variant|MODIFIER|ORF8|GU280_gp09|transcript|GU280_gp09|protein_coding||c.*1483G>T|||||1483|,T|downstream_gene_variant|MODIFIER|N|GU280_gp10|transcript|GU280_gp10|protein_coding||c.*209G>T|||||209|,T|downstream_gene_variant|MODIFIER|ORF10|GU280_gp11|transcript|GU280_gp11|protein_coding||c.*68G>T|||||68|,T|intergenic_region|MODIFIER|ORF10-CHR_END|GU280_gp11-CHR_END|intergenic_region|GU280_gp11-CHR_END|||n.29742G>T||||||	GT:DP:AD:RO:QR:AO:QA:GL	1/1:1276:0,1276:0:0:1276:44133:-3675.72,-384.114,0
