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view test-data/day_60.vcf @ 1:30584e80d61e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 5ae40d4f44fc2716f3c37a9fad2077a0d0230a6d
author iuc
date Mon, 03 Jun 2024 09:37:09 +0000
parents d2a1ac520392
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##fileformat=VCFv4.0
##fileDate=20220906
##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 20 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.001 --bonf dynamic --no-default-filter --no-default-filter -r NC_045512:1-7475 -o /data/jwd01/main/050/269/50269464/tmp/lofreq2_call_parallel15a3xw5c/0.vcf.gz reads.bam 
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_66,Description="Minimum SNV Quality (Phred) 66">
##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_58,Description="Minimum Indel Quality (Phred) 58">
##FILTER=<ID=min_af_0.100000,Description="Minimum allele frequency 0.100000">
##FILTER=<ID=min_dp_20,Description="Minimum Coverage 20">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##SnpEffVersion="4.3t (build 2017-11-24 10:18), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf -formatEff -classic -no-downstream -no-intergenic -no-intron -no-upstream -stats /data/jwd01/main/050/269/50269699/outputs/galaxy_dataset_4f76b3c9-c65b-440c-b6eb-7c0658803d91.dat -csvStats /data/jwd01/main/050/269/50269699/outputs/galaxy_dataset_80517e55-786a-45d8-bef0-754a8780e1a9.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/9/4/9/dataset_94943b16-6476-4636-83c0-5f7d8cfc524c.dat "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_Change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon_Rank  | Genotype [ | ERRORS | WARNINGS ] )' ">
##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
NC_045512	59	.	C	A	1760.0	PASS	AF=0.854545;DP=55;DP4=0,0,37,18;SB=0
NC_045512	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.978667;DP=1875;DP4=75,82,1053,782;HRUN=2;SB=16;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggtcatgttatg/gtg|GHVM82V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	670	.	T	G	42432.0	PASS	AF=0.920869;DP=1289;DP4=0,2,647,637;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	900	.	C	T	49314.0	PASS	AF=0.941725;DP=2145;DP4=0,1,1107,1034;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1821	.	G	A	1189.0	PASS	AF=0.125604;DP=414;DP4=159,197,31,27;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G519D|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	1980	.	G	T	8919.0	PASS	AF=0.895522;DP=268;DP4=0,0,134,134;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	19472.0	PASS	AF=0.935201;DP=571;DP4=1,1,278,288;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T842I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	3037	.	C	T	28976.0	PASS	AF=0.941805;DP=842;DP4=1,1,419,418;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	9009.0	PASS	AF=0.907407;DP=270;DP4=0,0,167,103;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G1307S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	4276	.	C	T	14849.0	PASS	AF=0.911565;DP=441;DP4=3,3,290,145;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	12472.0	PASS	AF=0.790068;DP=443;DP4=63,0,197,182;SB=159;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5628	.	C	T	17261.0	PASS	AF=0.911488;DP=531;DP4=2,1,237,289;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6048	.	T	C	1355.0	PASS	AF=0.155425;DP=341;DP4=141,141,30,29;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tTt/tCt|F1928S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
NC_045512	6083	.	G	T	751.0	PASS	AF=0.110000;DP=300;DP4=143,118,19,18;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D1940Y|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	8316.0	PASS	AF=0.771987;DP=307;DP4=48,0,157,100;SB=89;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	7246	.	G	GT	2323.0	PASS	AF=0.105200;DP=827;DP4=349,424,45,42;HRUN=5;SB=5;INDEL;EFF=FRAME_SHIFT(HIGH||ttg/ttTg|L2329F?|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|GT|INFO_REALIGN_3_PRIME);LOF=(ORF1ab|GU280_gp01|1|1.00)
NC_045512	8109	.	C	T	22999.0	PASS	AF=0.936937;DP=666;DP4=1,2,345,316;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T2615I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	8537	.	A	G	1413.0	PASS	AF=0.117647;DP=493;DP4=216,213,25,36;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I2758V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9344	.	C	T	46680.0	PASS	AF=0.949165;DP=1318;DP4=0,0,682,633;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3027F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9424	.	A	G	42834.0	PASS	AF=0.944844;DP=1251;DP4=0,1,635,614;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9534	.	C	T	49314.0	PASS	AF=0.940808;DP=2078;DP4=0,1,941,1132;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T3090I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9866	.	C	T	29696.0	PASS	AF=0.889010;DP=919;DP4=23,13,543,339;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10029	.	C	T	49314.0	PASS	AF=0.815325;DP=1814;DP4=0,9,851,950;SB=23;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	38164.0	PASS	AF=0.823036;DP=1311;DP4=65,61,619,561;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	22164.0	PASS	AF=0.884164;DP=682;DP4=1,0,330,347;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	21817.0	PASS	AF=0.863836;DP=683;DP4=0,7,336,337;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10687	.	TG	T	2233.0	PASS	AF=0.103405;DP=793;DP4=408,325,48,34;HRUN=1;SB=1;INDEL;EFF=FRAME_SHIFT(HIGH||gtt/|V3475|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T);LOF=(ORF1ab|GU280_gp01|1|1.00)
NC_045512	11287	.	GTCTGGTTTT	G	5267.0	PASS	AF=0.988764;DP=178;DP4=11,9,86,90;HRUN=1;SB=1;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	33687.0	PASS	AF=0.897411;DP=1043;DP4=0,0,506,531;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12854	.	C	T	17843.0	PASS	AF=0.868231;DP=554;DP4=0,0,297,257;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	20579.0	PASS	AF=0.948542;DP=583;DP4=0,0,295,286;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	49314.0	PASS	AF=0.941292;DP=1533;DP4=1,0,668,860;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	15451	.	G	A	28015.0	PASS	AF=0.827736;DP=923;DP4=1,1,546,368;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
NC_045512	15714	.	C	T	37696.0	PASS	AF=0.953774;DP=1060;DP4=0,0,510,545;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17137	.	T	C	3063.0	PASS	AF=0.134361;DP=908;DP4=402,366,77,56;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Cct|S5630P|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|C)
NC_045512	17410	.	C	T	10881.0	PASS	AF=0.893939;DP=330;DP4=0,0,164,163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgt/Tgt|R5721C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	18163	.	A	G	13707.0	PASS	AF=0.927536;DP=414;DP4=0,0,208,205;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	18778	.	TGGG	T	3602.0	PASS	AF=0.123062;DP=1032;DP4=415,495,56,71;HRUN=4;SB=1;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||tggggt/tgt|WG6177C|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T|INFO_REALIGN_3_PRIME)
NC_045512	19955	.	C	T	36425.0	PASS	AF=0.943961;DP=1035;DP4=0,0,521,511;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T6569I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	20055	.	A	G	9643.0	PASS	AF=0.897611;DP=293;DP4=14,0,127,151;SB=45;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	5731.0	PASS	AF=0.906977;DP=172;DP4=0,0,108,62;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21618	.	C	T	32230.0	PASS	AF=0.917204;DP=930;DP4=0,0,436,488;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	30504.0	PASS	AF=0.992299;DP=909;DP4=26,13,413,489;HRUN=2;SB=18;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21987	.	G	A	15467.0	PASS	AF=0.794340;DP=530;DP4=3,0,280,244;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	7938.0	PASS	AF=0.908333;DP=240;DP4=0,0,96,142;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTg/gGg|V213G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22578	.	G	A	27298.0	PASS	AF=0.891892;DP=851;DP4=0,0,414,434;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22629	.	A	C	24933.0	PASS	AF=0.903567;DP=757;DP4=1,0,356,400;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22664	.	C	A	24562.0	PASS	AF=0.917695;DP=729;DP4=1,2,307,414;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22674	.	C	T	21334.0	PASS	AF=0.846705;DP=698;DP4=0,4,285,408;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22679	.	T	C	22897.0	PASS	AF=0.938346;DP=665;DP4=0,0,267,397;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tca/Cca|S373P|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22686	.	C	T	19116.0	PASS	AF=0.869984;DP=623;DP4=0,2,262,358;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	19590.0	PASS	AF=0.901695;DP=590;DP4=0,0,249,340;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Act/Gct|T376A|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22716	.	C	T	16916.0	PASS	AF=0.941788;DP=481;DP4=1,1,224,254;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T385I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22775	.	G	A	27898.0	PASS	AF=0.691026;DP=1560;DP4=186,237,577,559;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22786	.	A	C	45143.0	PASS	AF=0.890287;DP=1431;DP4=0,1,760,664;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22792	.	C	T	49314.0	PASS	AF=0.931681;DP=1493;DP4=0,1,805,681;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I410|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22813	.	G	T	49314.0	PASS	AF=0.910685;DP=1825;DP4=0,1,1008,810;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22882	.	T	G	49314.0	PASS	AF=0.899664;DP=1784;DP4=2,2,1005,768;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22992	.	G	A	49314.0	PASS	AF=0.931250;DP=1760;DP4=1,1,767,986;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22995	.	C	A	49314.0	PASS	AF=0.953356;DP=1758;DP4=0,0,771,985;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aAa|T478K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23013	.	A	C	49314.0	PASS	AF=0.907710;DP=1712;DP4=5,3,734,967;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23040	.	A	G	49314.0	PASS	AF=0.895874;DP=1527;DP4=0,4,663,859;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23055	.	A	G	44772.0	PASS	AF=0.903039;DP=1382;DP4=2,1,608,770;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	47115.0	PASS	AF=0.939597;DP=1341;DP4=0,3,617,719;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23075	.	T	C	41610.0	PASS	AF=0.911007;DP=1281;DP4=1,0,619,660;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	8353.0	PASS	AF=0.939516;DP=248;DP4=1,0,116,131;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23525	.	C	T	7115.0	PASS	AF=0.871560;DP=218;DP4=0,1,102,113;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23599	.	T	G	22781.0	PASS	AF=0.932229;DP=664;DP4=0,0,346,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23604	.	C	A	22524.0	PASS	AF=0.925982;DP=662;DP4=1,1,345,313;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23854	.	C	A	11753.0	PASS	AF=0.933333;DP=345;DP4=0,3,173,169;SB=9;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23948	.	G	T	14977.0	PASS	AF=0.911364;DP=440;DP4=0,1,226,210;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24318	.	A	ACC	556.0	PASS	AF=0.107356;DP=503;DP4=226,224,27,27;HRUN=2;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||caa/cCCaa|Q920P?|1273|S|protein_coding|CODING|GU280_gp02|1|ACC|INFO_REALIGN_3_PRIME);LOF=(S|GU280_gp02|1|1.00)
NC_045512	24320	.	CAAA	C	548.0	PASS	AF=0.108652;DP=497;DP4=237,225,27,27;HRUN=5;SB=0;INDEL;EFF=CODON_DELETION(MODERATE||aaa/|K921|1273|S|protein_coding|CODING|GU280_gp02|1|C|INFO_REALIGN_3_PRIME)
NC_045512	24424	.	A	T	49314.0	PASS	AF=0.909987;DP=1522;DP4=0,5,853,661;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24469	.	T	A	49314.0	PASS	AF=0.922658;DP=1836;DP4=2,1,1000,830;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24951	.	TAG	T	3457.0	PASS	AF=0.100924;DP=1298;DP4=509,678,57,74;HRUN=1;SB=0;INDEL;EFF=FRAME_SHIFT(HIGH||atagga/|IG1130|1273|S|protein_coding|CODING|GU280_gp02|1|T);LOF=(S|GU280_gp02|1|1.00)
NC_045512	24966	.	A	G	41334.0	PASS	AF=0.887944;DP=1294;DP4=1,1,548,722;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	39557.0	PASS	AF=0.924282;DP=1149;DP4=0,0,560,586;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	49314.0	PASS	AF=0.816110;DP=1887;DP4=42,43,1024,772;SB=7;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	34411.0	PASS	AF=0.949640;DP=973;DP4=0,0,464,508;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	9159.0	PASS	AF=0.878893;DP=289;DP4=0,0,148,140;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26270	.	C	T	12517.0	PASS	AF=0.917808;DP=365;DP4=1,0,193,170;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26577	.	C	G	29585.0	PASS	AF=0.898210;DP=894;DP4=0,0,456,435;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512	26709	.	G	A	49314.0	PASS	AF=0.924149;DP=1938;DP4=2,0,982,939;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26801	.	C	T	49314.0	PASS	AF=0.889426;DP=1863;DP4=1,0,935,918;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	39423.0	PASS	AF=0.890110;DP=1183;DP4=1,2,564,608;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	27259	.	A	C	49314.0	PASS	AF=0.901362;DP=2129;DP4=1,2,859,1262;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	18534.0	PASS	AF=0.875886;DP=564;DP4=0,1,279,281;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27383	.	A	T	18084.0	PASS	AF=0.860465;DP=559;DP4=1,1,278,278;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512	27384	.	T	C	19016.0	PASS	AF=0.900709;DP=564;DP4=4,0,277,281;SB=9;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	T	23583.0	PASS	AF=0.956845;DP=672;DP4=2,0,317,353;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27549	.	C	T	49314.0	PASS	AF=0.888954;DP=1720;DP4=0,2,914,791;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	31266.0	PASS	AF=0.941694;DP=909;DP4=2,1,457,448;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L18|43|ORF7b|protein_coding|CODING|GU280_gp08|1|T)
NC_045512	28271	.	A	T	49314.0	PASS	AF=0.856293;DP=2185;DP4=3,14,1036,1059;SB=19
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.795816;DP=2581;DP4=60,65,1233,1220;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	48884.0	PASS	AF=0.710514;DP=2197;DP4=425,228,710,851;HRUN=2;SB=164;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ggagaacgcagt/ggt|GERS30G|419|N|protein_coding|CODING|GU280_gp10|1|G|INFO_REALIGN_3_PRIME)
NC_045512	28657	.	C	T	49314.0	PASS	AF=0.856894;DP=3445;DP4=30,41,1789,1544;SB=11;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	49314.0	PASS	AF=0.936155;DP=1441;DP4=0,1,675,763;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGg/aAg|R203K|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28882	.	G	A	47438.0	PASS	AF=0.895543;DP=1436;DP4=0,1,669,749;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	48607.0	PASS	AF=0.905024;DP=1453;DP4=0,0,674,774;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gga/Cga|G204R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29510	.	A	C	49314.0	PASS	AF=0.913119;DP=4017;DP4=2,5,1794,2208;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Agt/Cgt|S413R|419|N|protein_coding|CODING|GU280_gp10|1|C)
NC_045512	29733	.	CGAGGCCACGCGGAGTACGATCGAGTG	C	49314.0	PASS	AF=0.991364;DP=2200;DP4=197,163,758,1423;HRUN=1;SB=119;INDEL