view test-data/day_32.vcf @ 3:b5411b5e8259 draft default tip

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=20220830
##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/050/067/50067391/tmp/lofreq2_call_parallel84g9etws/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_63,Description="Minimum SNV Quality (Phred) 63">
##FILTER=<ID=min_indelqual_48,Description="Minimum Indel Quality (Phred) 48">
##FILTER=<ID=min_snvqual_71,Description="Minimum SNV Quality (Phred) 71">
##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/050/067/50067628/outputs/galaxy_dataset_776fff03-e254-4dfb-abbf-8d93b9cfb46b.dat -csvStats /data/jwd01/main/050/067/50067628/outputs/galaxy_dataset_fb58a8b5-8934-4d3e-9ea4-2b45f3933814.dat SARS-CoV-2 /data/dnb06/galaxy_db/files/7/6/b/dataset_76b4f78f-44ca-48ff-9ffb-46fda2231d70.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	15763.0	PASS	AF=0.991903;DP=494;DP4=25,25,293,197;HRUN=2;SB=6;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	19515.0	PASS	AF=0.969369;DP=555;DP4=0,0,280,275;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agT/agG|S135R|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	900	.	C	T	38595.0	PASS	AF=0.975285;DP=1052;DP4=5,2,514,531;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1980	.	G	T	10895.0	PASS	AF=0.966443;DP=298;DP4=0,0,153,144;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	15238.0	PASS	AF=0.966903;DP=423;DP4=0,0,204,219;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	26967.0	PASS	AF=0.966533;DP=747;DP4=0,0,361,383;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4184	.	G	A	10051.0	PASS	AF=0.978102;DP=274;DP4=0,0,162,112;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	10845.0	PASS	AF=0.983051;DP=295;DP4=0,0,216,79;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	6431.0	PASS	AF=0.716475;DP=261;DP4=65,3,103,90;SB=108;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5628	.	C	T	3005.0	PASS	AF=0.293011;DP=372;DP4=113,147,57,54;SB=7;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	7773.0	PASS	AF=0.760274;DP=292;DP4=66,1,132,93;SB=113;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	20585.0	PASS	AF=0.982206;DP=562;DP4=0,0,283,279;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	18743.0	PASS	AF=0.965779;DP=526;DP4=2,2,253,268;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9534	.	C	T	34480.0	PASS	AF=0.985808;DP=916;DP4=0,1,445,469;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	19606.0	PASS	AF=0.983114;DP=533;DP4=0,0,315,218;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	23751.0	PASS	AF=0.944035;DP=679;DP4=0,1,306,372;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCc/aTc|T3255I|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10198	.	C	T	19726.0	PASS	AF=0.990637;DP=534;DP4=0,0,281,253;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	11857.0	PASS	AF=0.951662;DP=331;DP4=0,0,164,165;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	11818.0	PASS	AF=0.954407;DP=329;DP4=0,1,164,163;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cAc|P3395H|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	11287	.	GTCTGGTTTT	G	6182.0	PASS	AF=0.994872;DP=195;DP4=21,21,89,105;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	18290.0	PASS	AF=0.963178;DP=516;DP4=0,0,258,258;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	14548.0	PASS	AF=0.967172;DP=396;DP4=1,2,200,193;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	14683.0	PASS	AF=0.984810;DP=395;DP4=0,0,197,198;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	39342.0	PASS	AF=0.971216;DP=1077;DP4=1,2,531,543;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cTt|P4720L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	15451	.	G	A	26255.0	PASS	AF=0.969655;DP=725;DP4=0,0,411,313;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	21454.0	PASS	AF=0.972789;DP=588;DP4=0,0,282,306;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	9474.0	PASS	AF=0.984496;DP=258;DP4=0,0,127,131;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	12021.0	PASS	AF=0.970326;DP=337;DP4=0,0,168,169;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	28596.0	PASS	AF=0.973180;DP=783;DP4=0,0,463,318;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	11442.0	PASS	AF=0.968051;DP=313;DP4=0,0,156,157;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	15802.0	PASS	AF=0.976798;DP=431;DP4=0,0,237,194;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21618	.	C	T	40675.0	PASS	AF=0.983441;DP=1087;DP4=1,2,533,551;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	32959.0	PASS	AF=0.983211;DP=953;DP4=39,46,461,476;HRUN=2;SB=2;INDEL;EFF=CODON_CHANGE_PLUS_CODON_DELETION(MODERATE||ttaccccctgca/tca|LPPA24S|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21691	.	C	T	4169.0	PASS	AF=0.155660;DP=1060;DP4=430,461,81,88;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F43|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21987	.	G	A	29742.0	PASS	AF=0.954816;DP=841;DP4=1,0,431,407;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	14370.0	PASS	AF=0.973105;DP=409;DP4=0,0,199,210;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	21245.0	PASS	AF=0.974790;DP=595;DP4=1,0,296,298;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22629	.	A	C	19866.0	PASS	AF=0.971377;DP=559;DP4=0,0,284,275;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	20854.0	PASS	AF=0.972028;DP=572;DP4=0,0,277,292;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	20794.0	PASS	AF=0.974315;DP=584;DP4=0,0,280,303;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S371F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22679	.	T	C	20993.0	PASS	AF=0.976190;DP=588;DP4=0,0,286,302;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	19322.0	PASS	AF=0.967332;DP=551;DP4=0,1,267,279;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCc/tTc|S375F|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22688	.	A	G	19389.0	PASS	AF=0.970588;DP=544;DP4=0,0,267,276;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	20710.0	PASS	AF=0.989267;DP=559;DP4=0,0,282,277;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	42814.0	PASS	AF=0.980375;DP=1172;DP4=2,6,574,590;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D405N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22786	.	A	C	43361.0	PASS	AF=0.963816;DP=1216;DP4=0,0,597,619;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|agA/agC|R408S|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22792	.	C	T	46048.0	PASS	AF=0.977689;DP=1255;DP4=0,0,614,641;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=0.978801;DP=1368;DP4=0,0,679,686;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaG/aaT|K417N|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	22882	.	T	G	38759.0	PASS	AF=0.966102;DP=1062;DP4=1,0,595,466;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	30675.0	PASS	AF=0.978873;DP=852;DP4=0,0,387,464;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	30708.0	PASS	AF=0.978495;DP=837;DP4=0,0,384,453;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	30583.0	PASS	AF=0.974760;DP=832;DP4=0,0,377,454;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23040	.	A	G	29750.0	PASS	AF=0.985240;DP=813;DP4=0,0,371,442;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	28119.0	PASS	AF=0.969620;DP=790;DP4=1,2,367,420;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	27561.0	PASS	AF=0.990553;DP=741;DP4=0,0,359,382;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	26731.0	PASS	AF=0.960681;DP=763;DP4=2,2,379,380;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	14034.0	PASS	AF=0.966752;DP=391;DP4=0,0,179,212;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	14033.0	PASS	AF=0.981771;DP=384;DP4=0,0,204,180;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cat/Tat|H655Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	23589	.	C	A	5160.0	PASS	AF=0.188293;DP=1025;DP4=439,391,104,90;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aAt|T676N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23599	.	T	G	38164.0	PASS	AF=0.969466;DP=1048;DP4=0,1,549,497;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N679K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23604	.	C	A	38022.0	PASS	AF=0.982592;DP=1034;DP4=0,1,541,490;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23854	.	C	A	21304.0	PASS	AF=0.960000;DP=600;DP4=0,1,283,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaC/aaA|N764K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23948	.	G	T	22285.0	PASS	AF=0.971901;DP=605;DP4=0,0,315,290;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Tat|D796Y|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24424	.	A	T	48760.0	PASS	AF=0.975392;DP=1341;DP4=1,1,682,657;SB=0;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=0.966245;DP=1422;DP4=0,2,719,698;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	30117.0	PASS	AF=0.970203;DP=839;DP4=0,0,399,437;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	32463.0	PASS	AF=0.964126;DP=892;DP4=0,1,436,454;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	37535.0	PASS	AF=0.959499;DP=1037;DP4=0,1,579,457;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	43542.0	PASS	AF=0.979644;DP=1179;DP4=0,0,582,596;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	18449.0	PASS	AF=0.959770;DP=522;DP4=1,0,262,258;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	20039.0	PASS	AF=0.965704;DP=554;DP4=2,3,280,269;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26408	.	C	T	24554.0	PASS	AF=0.633469;DP=1225;DP4=225,182,408,383;SB=6;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26577	.	C	G	24616.0	PASS	AF=0.974889;DP=677;DP4=2,1,309,364;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Caa/Gaa|Q19E|222|M|protein_coding|CODING|GU280_gp05|1|G)
NC_045512	26709	.	G	A	47953.0	PASS	AF=0.966641;DP=1319;DP4=0,0,741,577;SB=0;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=0.973983;DP=1499;DP4=0,1,758,740;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	49314.0	PASS	AF=0.988078;DP=1342;DP4=0,0,605,737;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F112|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	27259	.	A	C	47693.0	PASS	AF=0.965004;DP=1343;DP4=3,5,560,770;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	14516.0	PASS	AF=0.971795;DP=390;DP4=0,0,187,201;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	14641.0	PASS	AF=0.981959;DP=388;DP4=0,0,187,201;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	14550.0	PASS	AF=0.972010;DP=393;DP4=0,0,189,202;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	T	16357.0	PASS	AF=0.977728;DP=449;DP4=0,0,230,219;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	36762.0	PASS	AF=0.980080;DP=1004;DP4=1,0,512,489;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	22385.0	PASS	AF=0.978723;DP=611;DP4=1,1,311,298;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=0.973483;DP=1697;DP4=0,1,853,843;SB=3
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.939506;DP=1620;DP4=0,2,794,819;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	37520.0	PASS	AF=0.786337;DP=1376;DP4=247,53,394,688;HRUN=2;SB=465;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	45171.0	PASS	AF=0.964511;DP=1268;DP4=1,1,668,597;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	20403.0	PASS	AF=0.960714;DP=560;DP4=1,1,271,287;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	19828.0	PASS	AF=0.942755;DP=559;DP4=0,0,271,287;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	20716.0	PASS	AF=0.970280;DP=572;DP4=0,0,277,295;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=0.966520;DP=1822;DP4=0,0,792,1028;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	21485.0	PASS	AF=0.981550;DP=542;DP4=94,101,189,343;HRUN=1;SB=25;INDEL