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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virheat commit 8f495733edea9287f6392a893c9429fd16b1cb1d
author | iuc |
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date | Mon, 26 Aug 2024 18:10:25 +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/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