Mercurial > repos > iuc > virheat

##fileformat=VCFv4.0
##fileDate=20220927
##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/050/996/50996340/tmp/lofreq2_call_parallel6ivdou83/0.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_59,Description="Minimum Indel Quality (Phred) 59">
##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/jwd/main/050/996/50996575/outputs/galaxy_dataset_75872de2-697f-40a3-8fc1-615981f550e3.dat -csvStats /data/jwd/main/050/996/50996575/outputs/galaxy_dataset_5f2c1e84-2d8b-4128-b50b-2f94725c3fa8.dat SARS-CoV-2 /data/dnb07/galaxy_db/files/4/4/b/dataset_44b78fc2-2fd9-4e6c-91ce-81aba326a225.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	21124.0	PASS	AF=0.984195;DP=696;DP4=32,39,423,262;HRUN=2;SB=21;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	19287.0	PASS	AF=0.922680;DP=582;DP4=1,1,272,307;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	49314.0	PASS	AF=0.937765;DP=1414;DP4=2,1,730,675;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S212L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	1980	.	G	T	7272.0	PASS	AF=0.865217;DP=230;DP4=0,1,115,113;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGa/gTa|G572V|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	2790	.	C	T	9638.0	PASS	AF=0.925795;DP=283;DP4=0,0,135,145;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	21293.0	PASS	AF=0.960133;DP=602;DP4=0,1,299,302;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ttC/ttT|F924|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	3683	.	C	A	238.0	PASS	AF=0.105263;DP=95;DP4=49,36,6,4;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Aag|Q1140K|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	4184	.	G	A	9755.0	PASS	AF=0.925532;DP=282;DP4=0,0,172,109;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	8500.0	PASS	AF=0.882576;DP=264;DP4=0,0,210,53;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|taC/taT|Y1337|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	4321	.	C	T	3039.0	PASS	AF=0.375000;DP=280;DP4=166,2,60,52;SB=217;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcC/gcT|A1352|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	5302	.	A	G	14543.0	PASS	AF=0.849899;DP=493;DP4=12,15,227,233;SB=1;EFF=SYNONYMOUS_CODING(LOW|SILENT|gcA/gcG|A1679|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	5628	.	C	T	6181.0	PASS	AF=0.870647;DP=201;DP4=1,0,99,98;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCg/aTg|T1788M|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	6354	.	C	T	4745.0	PASS	AF=0.496667;DP=300;DP4=136,0,97,67;SB=209;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCa/tTa|S2030L|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	9344	.	C	T	14163.0	PASS	AF=0.929612;DP=412;DP4=0,0,204,205;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	16090.0	PASS	AF=0.906504;DP=492;DP4=0,1,250,237;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|gtA/gtG|V3053|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	9534	.	C	T	30931.0	PASS	AF=0.851434;DP=976;DP4=0,0,476,492;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	21641.0	PASS	AF=0.936204;DP=627;DP4=2,3,352,268;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Ttt|L3201F|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10029	.	C	T	24390.0	PASS	AF=0.919220;DP=718;DP4=0,0,327,385;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	13719.0	PASS	AF=0.859447;DP=434;DP4=0,0,227,200;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D3311|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	10447	.	G	A	6728.0	PASS	AF=0.915000;DP=200;DP4=0,0,101,99;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R3394|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|A)
NC_045512	10449	.	C	A	6479.0	PASS	AF=0.875000;DP=200;DP4=1,0,101,97;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	5414.0	PASS	AF=0.988372;DP=172;DP4=12,15,87,83;HRUN=1;SB=2;INDEL;EFF=CODON_DELETION(MODERATE||tctggtttt/|SGF3675|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|G)
NC_045512	12036	.	C	T	13967.0	PASS	AF=0.908879;DP=428;DP4=0,0,191,236;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	8084.0	PASS	AF=0.850980;DP=255;DP4=1,4,121,129;SB=4;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cct/Tct|P4197S|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	12880	.	C	T	9293.0	PASS	AF=0.953668;DP=259;DP4=0,0,122,137;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|atC/atT|I4205|7101|ORF1ab|protein_coding|CODING|GU280_gp01|1|T)
NC_045512	14408	.	C	T	30442.0	PASS	AF=0.945790;DP=867;DP4=1,1,421,444;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	32619.0	PASS	AF=0.917191;DP=954;DP4=2,0,570,378;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	16193.0	PASS	AF=0.944326;DP=467;DP4=0,0,232,235;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L5155|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	17410	.	C	T	4679.0	PASS	AF=0.927007;DP=137;DP4=0,0,61,76;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	8692.0	PASS	AF=0.853147;DP=286;DP4=1,2,138,143;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	34314.0	PASS	AF=0.954825;DP=974;DP4=0,1,461,509;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	4430.0	PASS	AF=0.811321;DP=159;DP4=21,1,66,71;SB=48;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaA/gaG|E6602|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|G)
NC_045512	20719	.	C	T	8638.0	PASS	AF=0.950820;DP=244;DP4=1,1,135,107;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|Cta/Tta|L6824|7101|ORF1ab|protein_coding|CODING|GU280_gp01|2|T)
NC_045512	21618	.	C	T	23086.0	PASS	AF=0.871329;DP=715;DP4=0,2,339,365;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T19I|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	21632	.	TTACCCCCTG	T	20809.0	PASS	AF=0.990581;DP=637;DP4=37,20,286,345;HRUN=2;SB=22;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	27221.0	PASS	AF=0.915545;DP=817;DP4=2,0,449,362;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G142D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22200	.	T	G	11644.0	PASS	AF=0.940120;DP=334;DP4=0,0,146,188;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	11598.0	PASS	AF=0.782082;DP=413;DP4=0,1,190,214;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gGt/gAt|G339D|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22599	.	G	C	10927.0	PASS	AF=0.865330;DP=349;DP4=0,0,163,183;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGa/aCa|R346T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	22629	.	A	C	10965.0	PASS	AF=0.875000;DP=352;DP4=0,0,160,192;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	10461.0	PASS	AF=0.896552;DP=319;DP4=1,0,139,176;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cta/Ata|L368I|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22674	.	C	T	10533.0	PASS	AF=0.945338;DP=311;DP4=0,0,142,169;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	10381.0	PASS	AF=0.919872;DP=312;DP4=0,0,146,164;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	9882.0	PASS	AF=0.922297;DP=296;DP4=1,2,139,152;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	9752.0	PASS	AF=0.880645;DP=310;DP4=0,0,149,159;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	10414.0	PASS	AF=0.923588;DP=301;DP4=0,0,156,141;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	32099.0	PASS	AF=0.611635;DP=2544;DP4=422,472,857,792;SB=16;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=0.911746;DP=1541;DP4=3,6,803,727;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=0.944075;DP=1502;DP4=1,0,788,709;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=0.928571;DP=1610;DP4=1,0,841,763;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	32587.0	PASS	AF=0.774221;DP=1156;DP4=8,5,629,510;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaG|N440K|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	22992	.	G	A	31454.0	PASS	AF=0.921758;DP=933;DP4=1,0,411,514;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aGc/aAc|S477N|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	22995	.	C	A	33366.0	PASS	AF=0.967672;DP=928;DP4=0,0,417,509;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	32717.0	PASS	AF=0.891304;DP=1012;DP4=6,5,461,535;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|gAa/gCa|E484A|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23040	.	A	G	33801.0	PASS	AF=0.914086;DP=1001;DP4=0,2,465,528;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q493R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23055	.	A	G	31971.0	PASS	AF=0.904908;DP=978;DP4=0,2,465,509;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cAa/cGa|Q498R|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	23063	.	A	T	34081.0	PASS	AF=0.953271;DP=963;DP4=0,0,466,496;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	30581.0	PASS	AF=0.886715;DP=971;DP4=7,0,480,481;SB=18;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tac/Cac|Y505H|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23403	.	A	G	6624.0	PASS	AF=0.937500;DP=192;DP4=0,1,88,103;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	5738.0	PASS	AF=0.885057;DP=174;DP4=0,0,87,85;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	34087.0	PASS	AF=0.924623;DP=995;DP4=2,2,543,443;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	32266.0	PASS	AF=0.891019;DP=991;DP4=0,7,541,438;SB=24;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCt/cAt|P681H|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	23781	.	T	C	19378.0	PASS	AF=0.926829;DP=574;DP4=0,0,258,315;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M740T|1273|S|protein_coding|CODING|GU280_gp02|1|C)
NC_045512	23854	.	C	A	15863.0	PASS	AF=0.935484;DP=465;DP4=1,1,224,237;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	14150.0	PASS	AF=0.882217;DP=433;DP4=0,0,213,209;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	34766.0	PASS	AF=0.852834;DP=1094;DP4=0,17,579,496;SB=56;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|caA/caT|Q954H|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	24469	.	T	A	40157.0	PASS	AF=0.926871;DP=1176;DP4=8,0,614,554;SB=20;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aaT/aaA|N969K|1273|S|protein_coding|CODING|GU280_gp02|1|A)
NC_045512	24966	.	A	G	15404.0	PASS	AF=0.884058;DP=483;DP4=0,3,223,250;SB=5;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAc/aGc|N1135S|1273|S|protein_coding|CODING|GU280_gp02|1|G)
NC_045512	25000	.	C	T	14885.0	PASS	AF=0.932870;DP=432;DP4=0,0,207,224;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D1146|1273|S|protein_coding|CODING|GU280_gp02|1|T)
NC_045512	25584	.	C	T	31362.0	PASS	AF=0.853000;DP=1000;DP4=2,13,580,402;SB=31;EFF=SYNONYMOUS_CODING(LOW|SILENT|acC/acT|T64|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26060	.	C	T	47532.0	PASS	AF=0.955157;DP=1338;DP4=1,2,679,652;SB=2;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCt/aTt|T223I|275|ORF3a|protein_coding|CODING|GU280_gp03|1|T)
NC_045512	26195	.	C	T	14674.0	PASS	AF=0.876356;DP=461;DP4=0,0,225,233;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	14524.0	PASS	AF=0.882353;DP=442;DP4=0,0,233,207;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aCa/aTa|T9I|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26408	.	C	T	33813.0	PASS	AF=0.922710;DP=1048;DP4=1,1,506,514;SB=0;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S55F|75|E|protein_coding|CODING|GU280_gp04|1|T)
NC_045512	26577	.	C	G	16529.0	PASS	AF=0.903808;DP=499;DP4=1,2,247,245;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	45733.0	PASS	AF=0.942308;DP=1300;DP4=0,1,719,575;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	44080.0	PASS	AF=0.932558;DP=1290;DP4=1,3,645,637;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|ctC/ctT|L93|222|M|protein_coding|CODING|GU280_gp05|1|T)
NC_045512	26858	.	C	T	37583.0	PASS	AF=0.949763;DP=1055;DP4=0,2,470,579;SB=2;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=0.894131;DP=1823;DP4=3,9,728,1075;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|Agg/Cgg|R20|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27382	.	G	C	14584.0	PASS	AF=0.904651;DP=430;DP4=1,0,211,214;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Cat|D61H|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27383	.	A	T	13812.0	PASS	AF=0.862150;DP=428;DP4=0,1,214,211;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	13802.0	PASS	AF=0.844037;DP=436;DP4=1,3,216,215;SB=2;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaT/gaC|D61|61|ORF6|protein_coding|CODING|GU280_gp06|1|C)
NC_045512	27481	.	C	A	18804.0	PASS	AF=0.951402;DP=535;DP4=2,0,272,259;SB=3;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctt/Att|L30I|121|ORF7a|protein_coding|CODING|GU280_gp07|1|A)
NC_045512	27549	.	C	T	45982.0	PASS	AF=0.876333;DP=1407;DP4=1,1,717,658;SB=0;EFF=SYNONYMOUS_CODING(LOW|SILENT|aaC/aaT|N52|121|ORF7a|protein_coding|CODING|GU280_gp07|1|T)
NC_045512	27807	.	C	T	18061.0	PASS	AF=0.931035;DP=522;DP4=0,0,252,269;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=0.915477;DP=1751;DP4=1,17,884,845;SB=42
NC_045512	28307	.	G	A	49314.0	PASS	AF=0.796053;DP=1824;DP4=5,3,896,871;SB=1;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gca/Aca|A12T|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28311	.	C	T	49314.0	PASS	AF=0.756948;DP=1835;DP4=2,45,917,862;SB=114;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|cCc/cTc|P13L|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28361	.	GGAGAACGCA	G	40606.0	PASS	AF=0.766583;DP=1598;DP4=305,87,454,771;HRUN=2;SB=455;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	28483	.	A	G	24461.0	PASS	AF=0.905512;DP=762;DP4=1,4,364,386;SB=4;EFF=SYNONYMOUS_CODING(LOW|SILENT|caA/caG|Q70|419|N|protein_coding|CODING|GU280_gp10|1|G)
NC_045512	28657	.	C	T	49314.0	PASS	AF=0.916149;DP=2254;DP4=1,3,1298,932;SB=5;EFF=SYNONYMOUS_CODING(LOW|SILENT|gaC/gaT|D128|419|N|protein_coding|CODING|GU280_gp10|1|T)
NC_045512	28881	.	G	A	30935.0	PASS	AF=0.969194;DP=844;DP4=0,0,406,437;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	28482.0	PASS	AF=0.916667;DP=840;DP4=0,2,402,433;SB=3;EFF=SYNONYMOUS_CODING(LOW|SILENT|agG/agA|R203|419|N|protein_coding|CODING|GU280_gp10|1|A)
NC_045512	28883	.	G	C	28643.0	PASS	AF=0.906033;DP=862;DP4=0,1,415,438;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=0.892053;DP=2177;DP4=1,1,945,1228;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	38545.0	PASS	AF=0.984359;DP=959;DP4=153,130,300,644;HRUN=1;SB=105;INDEL
author	iuc
date	Mon, 03 Jun 2024 09:37:09 +0000
parents	d2a1ac520392
children