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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
author iuc
date Mon, 26 Aug 2024 18:10:25 +0000
parents d2a1ac520392
children
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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/jwd/main/050/269/50269469/tmp/lofreq2_call_parallelcuwr5kal/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_65,Description="Minimum SNV Quality (Phred) 65">
##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48">
##FILTER=<ID=min_snvqual_74,Description="Minimum SNV Quality (Phred) 74">
##FILTER=<ID=min_indelqual_57,Description="Minimum Indel Quality (Phred) 57">
##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/050/269/50269704/outputs/galaxy_dataset_1406dfab-b1f3-45c3-a9b6-bac554061078.dat -csvStats /data/jwd01/main/050/269/50269704/outputs/galaxy_dataset_48d91a15-1687-4370-a8bf-80a1ae5e324e.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/1/e/8/dataset_1e8a611f-9522-456d-aa71-f8aa0c52bd75.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	509	.	GGTCATGTTA	G	49314.0	PASS	AF=0.950231;DP=1728;DP4=106,95,958,684;HRUN=2;SB=8;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	39786.0	PASS	AF=0.922306;DP=1197;DP4=0,0,576,617;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	751	.	C	T	3293.0	PASS	AF=0.111922;DP=1233;DP4=536,543,78,75;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N162|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	900	.	C	T	49314.0	PASS	AF=0.938511;DP=1854;DP4=1,0,961,891;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1238	.	C	T	9465.0	PASS	AF=0.327919;DP=985;DP4=294,335,170,184;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H325Y|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1980	.	G	T	5469.0	PASS	AF=0.886905;DP=168;DP4=1,1,82,82;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	8824.0	PASS	AF=0.937008;DP=254;DP4=1,1,119,131;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	25966.0	PASS	AF=0.934927;DP=753;DP4=4,3,376,367;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	6923.0	PASS	AF=0.877934;DP=213;DP4=0,0,115,98;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	4760.0	PASS	AF=0.948529;DP=136;DP4=0,0,108,28;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	1017.0	PASS	AF=0.387097;DP=93;DP4=53,1,24,15;SB=54;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	5868.0	PASS	AF=0.848958;DP=192;DP4=11,0,110,70;SB=21;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	29191.0	PASS	AF=0.957265;DP=819;DP4=0,0,417,399;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	25822.0	PASS	AF=0.949062;DP=746;DP4=0,0,372,373;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9495	.	T	C	25358.0	PASS	AF=0.858709;DP=821;DP4=4,59,411,347;SB=142;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTa/gCa|V3077A|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|C)
NC_045512	9534	.	C	T	38418.0	PASS	AF=0.938588;DP=1091;DP4=0,0,382,707;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	18168.0	PASS	AF=0.938697;DP=522;DP4=1,0,335,184;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	27199.0	PASS	AF=0.863046;DP=847;DP4=0,4,525,315;SB=16;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	26940.0	PASS	AF=0.910224;DP=802;DP4=3,2,415,381;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	16847.0	PASS	AF=0.869732;DP=522;DP4=2,0,252,265;SB=6;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	17359.0	PASS	AF=0.891841;DP=527;DP4=0,2,257,264;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	11287	.	GTCTGGTTTT	G	9083.0	PASS	AF=0.976898;DP=303;DP4=19,16,144,152;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12015	.	T	G	1187.0	PASS	AF=0.117096;DP=427;DP4=160,210,23,34;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gTt/gGt|V3917G|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	11567.0	PASS	AF=0.903955;DP=354;DP4=0,0,158,196;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gCt/gTt|A3924V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12342	.	C	T	16756.0	PASS	AF=0.680999;DP=721;DP4=175,24,312,206;SB=130;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T4026I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12854	.	C	T	13148.0	PASS	AF=0.882793;DP=401;DP4=0,0,217,183;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	14431.0	PASS	AF=0.955112;DP=401;DP4=0,0,212,189;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	38296.0	PASS	AF=0.938588;DP=1091;DP4=1,1,547,540;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	14724	.	C	T	45290.0	PASS	AF=0.927526;DP=1366;DP4=4,2,634,714;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F4825|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	15451	.	G	A	31057.0	PASS	AF=0.811966;DP=1053;DP4=2,0,634,407;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G5068S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|A)
NC_045512	15714	.	C	T	38183.0	PASS	AF=0.933817;DP=1103;DP4=10,12,517,558;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	4056.0	PASS	AF=0.925000;DP=120;DP4=0,0,57,62;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	7395.0	PASS	AF=0.860169;DP=236;DP4=0,0,123,113;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ata/Gta|I5972V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	19955	.	C	T	42798.0	PASS	AF=0.914877;DP=1257;DP4=2,1,658,594;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	12436.0	PASS	AF=0.904000;DP=375;DP4=19,0,135,221;SB=76;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	11814.0	PASS	AF=0.891061;DP=358;DP4=2,0,237,117;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21618	.	C	T	39403.0	PASS	AF=0.913234;DP=1141;DP4=0,1,553,574;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	37561.0	PASS	AF=0.993778;DP=1125;DP4=8,18,541,577;HRUN=2;SB=9;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	15152.0	PASS	AF=0.850932;DP=483;DP4=1,0,234,247;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	5164.0	PASS	AF=0.947368;DP=152;DP4=0,0,67,85;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	37640.0	PASS	AF=0.877238;DP=1173;DP4=2,1,560,602;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22599	.	G	C	39078.0	PASS	AF=0.952338;DP=1112;DP4=1,0,537,572;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22629	.	A	C	35645.0	PASS	AF=0.919508;DP=1056;DP4=0,0,517,539;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aCg|K356T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22664	.	C	A	34060.0	PASS	AF=0.896585;DP=1025;DP4=5,0,439,566;SB=17;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22674	.	C	T	28971.0	PASS	AF=0.812753;DP=988;DP4=0,4,411,568;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	31759.0	PASS	AF=0.929487;DP=936;DP4=0,0,390,543;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	26369.0	PASS	AF=0.863477;DP=857;DP4=0,4,360,487;SB=8;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	27392.0	PASS	AF=0.903148;DP=826;DP4=0,1,357,468;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	23123.0	PASS	AF=0.952087;DP=647;DP4=0,1,303,342;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	41610.0	PASS	AF=0.817662;DP=1574;DP4=83,112,686,691;SB=11;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22786	.	A	C	49314.0	PASS	AF=0.888278;DP=1638;DP4=1,3,841,788;SB=4;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=0.910736;DP=1658;DP4=1,0,856,799;SB=0;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=0.906464;DP=1903;DP4=7,1,1033,861;SB=11;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=0.892879;DP=1643;DP4=5,3,943,686;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=0.934586;DP=1544;DP4=0,1,654,884;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=0.948320;DP=1548;DP4=0,1,659,884;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=0.890767;DP=1538;DP4=11,9,637,874;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	46108.0	PASS	AF=0.904110;DP=1387;DP4=1,2,597,785;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23055	.	A	G	40054.0	PASS	AF=0.895414;DP=1243;DP4=2,1,556,682;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	42199.0	PASS	AF=0.936364;DP=1210;DP4=0,1,558,649;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Aat/Tat|N501Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23075	.	T	C	38081.0	PASS	AF=0.903501;DP=1171;DP4=1,0,570,598;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23278	.	T	C	13812.0	PASS	AF=0.380259;DP=1236;DP4=287,451,192,302;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|acT/acC|T572|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	16603.0	PASS	AF=0.913894;DP=511;DP4=1,1,220,287;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gGt|D614G|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23525	.	C	T	11697.0	PASS	AF=0.902299;DP=348;DP4=0,0,168,179;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	36022.0	PASS	AF=0.914953;DP=1070;DP4=4,4,556,505;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	35013.0	PASS	AF=0.891791;DP=1072;DP4=1,0,551,512;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	20324.0	PASS	AF=0.863706;DP=653;DP4=7,9,323,314;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23948	.	G	T	26988.0	PASS	AF=0.869928;DP=838;DP4=7,11,424,394;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24424	.	A	T	49314.0	PASS	AF=0.896979;DP=2019;DP4=1,10,1115,887;SB=24;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=0.919902;DP=2447;DP4=3,0,1307,1129;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	41768.0	PASS	AF=0.907801;DP=1269;DP4=2,2,550,708;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	37059.0	PASS	AF=0.908842;DP=1097;DP4=1,1,527,565;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	48242.0	PASS	AF=0.852652;DP=1527;DP4=2,7,893,621;SB=14;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	30995.0	PASS	AF=0.955326;DP=873;DP4=0,0,411,462;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	6504.0	PASS	AF=0.864734;DP=207;DP4=2,0,98,106;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T268M|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26270	.	C	T	7692.0	PASS	AF=0.914798;DP=223;DP4=0,0,114,107;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26333	.	C	T	6516.0	PASS	AF=0.921053;DP=190;DP4=0,0,101,89;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T30I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26542	.	C	T	2537.0	PASS	AF=0.128571;DP=840;DP4=367,338,65,53;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T7I|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26577	.	C	G	34567.0	PASS	AF=0.905314;DP=1035;DP4=0,0,507,523;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512	26625	.	C	T	39521.0	PASS	AF=0.955896;DP=1111;DP4=1,0,525,576;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L35|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26709	.	G	A	49314.0	PASS	AF=0.924801;DP=2008;DP4=11,9,985,995;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gct/Act|A63T|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26754	.	G	A	43115.0	PASS	AF=0.630244;DP=2050;DP4=305,308,724,707;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ggt/Agt|G78S|222|M|protein_coding|CODING|GU280_gp05|1|A)
NC_045512	26801	.	C	T	49314.0	PASS	AF=0.894977;DP=1752;DP4=11,10,842,884;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	33747.0	PASS	AF=0.875120;DP=1041;DP4=6,7,459,562;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=0.884010;DP=2095;DP4=8,15,817,1249;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	20379.0	PASS	AF=0.919056;DP=593;DP4=0,0,292,297;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	19296.0	PASS	AF=0.873720;DP=586;DP4=1,0,289,292;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAt/gTt|D61V|61|ORF6|protein_coding|CODING|GU280_gp06|1|T)
NC_045512	27384	.	T	C	20584.0	PASS	AF=0.917647;DP=595;DP4=0,0,298,297;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	T	24969.0	PASS	AF=0.942577;DP=714;DP4=0,0,348,364;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L30F|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27549	.	C	T	42569.0	PASS	AF=0.899366;DP=1262;DP4=0,0,625,635;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	18628.0	PASS	AF=0.947269;DP=531;DP4=1,0,257,269;SB=3;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=0.893357;DP=2213;DP4=2,12,1098,1083;SB=21
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.806593;DP=2518;DP4=14,27,1260,1205;SB=14;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	46560.0	PASS	AF=0.712057;DP=2115;DP4=428,205,665,841;HRUN=2;SB=226;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=0.863677;DP=3389;DP4=12,16,1835,1497;SB=5;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=0.943852;DP=1407;DP4=0,1,620,782;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	45952.0	PASS	AF=0.889522;DP=1403;DP4=1,0,618,772;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	48422.0	PASS	AF=0.927208;DP=1415;DP4=0,0,623,789;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=0.916667;DP=4344;DP4=2,2,1880,2446;SB=0;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=0.990955;DP=1990;DP4=174,138,681,1291;HRUN=1;SB=117;INDEL