Mercurial > repos > iuc > vsnp_determine_ref_from_data
view test-data/SRR1792272_zc.vcf @ 4:e3016c6c5994 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vsnp commit 95b221f68d19702681babd765c67caeeb24e7f1d"
| author | iuc |
|---|---|
| date | Tue, 16 Nov 2021 08:28:27 +0000 |
| parents | |
| children |
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##fileformat=VCFv4.2 ##fileDate=20190125 ##source=freeBayes v1.2.0-dirty ##reference=/scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1792272/NC_002945v4.fasta ##contig=<ID=NC_002945.4,length=4349904> ##phasing=none ##commandline="freebayes -E -1 -e 1 -u --strict-vcf -f /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1792272/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR1792272/SRR1792272-nodup.bam --region NC_002945.4:0-100000 ##filter="QUAL > 20 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype"> ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy"> ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele"> ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count"> ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations"> ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count"> ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block."> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SRR1792272 NC_002945.4 1057 . A G 8671.65 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=288;CIGAR=1X;DP=289;DPB=289;DPRA=0;EPP=3.04046;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=403.858;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9688;QR=0;RO=0;RPL=157;RPP=8.10723;RPPR=0;RPR=131;RUN=1;SAF=146;SAP=3.13094;SAR=142;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:289:0,288:0:0:288:9688:-871.673,-86.6966,0 NC_002945.4 29471 . N . . . . GT ./. NC_002945.4 29472 . N . . . . GT ./. NC_002945.4 29473 . N . . . . GT ./. NC_002945.4 29474 . N . . . . GT ./. NC_002945.4 29475 . N . . . . GT ./. NC_002945.4 29476 . N . . . . GT ./. NC_002945.4 29477 . N . . . . GT ./. NC_002945.4 29478 . N . . . . GT ./. NC_002945.4 29479 . N . . . . GT ./. NC_002945.4 41228 . A C 8160.68 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=279;CIGAR=1X;DP=286;DPB=286;DPRA=0;EPP=12.5445;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=356.696;PAIRED=0.992832;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=9191;QR=99;RO=7;RPL=131;RPP=5.2596;RPPR=3.32051;RPR=148;RUN=1;SAF=140;SAP=3.01808;SAR=139;SRF=0;SRP=18.2106;SRR=7;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:286:7,279:7:99:279:9191:-817.976,-77.0432,0 NC_002945.4 151025 . N . . . . GT ./. NC_002945.4 151026 . N . . . . GT ./. NC_002945.4 151027 . N . . . . GT ./. NC_002945.4 151028 . N . . . . GT ./. NC_002945.4 151029 . N . . . . GT ./. NC_002945.4 151030 . N . . . . GT ./. NC_002945.4 151031 . N . . . . GT ./. NC_002945.4 151032 . N . . . . GT ./. NC_002945.4 151033 . N . . . . GT ./. NC_002945.4 151034 . N . . . . GT ./. NC_002945.4 179885 . G A 5857.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=209;CIGAR=1X;DP=214;DPB=214;DPRA=0;EPP=6.01296;EPPR=11.6962;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=60;NS=1;NUMALT=1;ODDS=277.033;PAIRED=0.990431;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6578;QR=49;RO=4;RPL=106;RPP=3.10381;RPPR=5.18177;RPR=103;RUN=1;SAF=108;SAP=3.5194;SAR=101;SRF=3;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:214:4,209:4:49:209:6578:-587.486,-59.7074,0 NC_002945.4 306695 . N . . . . GT ./. NC_002945.4 306696 . N . . . . GT ./. NC_002945.4 306697 . N . . . . GT ./. NC_002945.4 306698 . N . . . . GT ./. NC_002945.4 306699 . N . . . . GT ./. NC_002945.4 306700 . N . . . . GT ./. NC_002945.4 306701 . N . . . . GT ./. NC_002945.4 306702 . N . . . . GT ./. NC_002945.4 306703 . N . . . . GT ./. NC_002945.4 306704 . N . . . . GT ./. NC_002945.4 319911 . C T 5833.3 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=187;CIGAR=1X;DP=189;DPB=189;DPRA=0;EPP=3.95088;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=59.9412;MQMR=0;NS=1;NUMALT=1;ODDS=263.842;PAIRED=0.989305;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6529;QR=0;RO=0;RPL=101;RPP=5.62303;RPPR=0;RPR=86;RUN=1;SAF=95;SAP=3.11481;SAR=92;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:189:0,187:0:0:187:6529:-587.398,-56.2926,0 NC_002945.4 332160 . N . . . . GT ./. NC_002945.4 332161 . N . . . . GT ./. NC_002945.4 332162 . N . . . . GT ./. NC_002945.4 332163 . N . . . . GT ./. NC_002945.4 332164 . N . . . . GT ./. NC_002945.4 332165 . N . . . . GT ./. NC_002945.4 332166 . N . . . . GT ./. NC_002945.4 332167 . N . . . . GT ./. NC_002945.4 332168 . N . . . . GT ./. NC_002945.4 332169 . N . . . . GT ./. NC_002945.4 332215 . C G 534.316 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=23;CIGAR=1X;DP=23;DPB=23;DPRA=0;EPP=52.9542;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.4899;PAIRED=0.913043;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=821;QR=0;RO=0;RPL=0;RPP=52.9542;RPPR=0;RPR=23;RUN=1;SAF=23;SAP=52.9542;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:23:0,23:0:0:23:821:-74.2027,-6.92369,0 NC_002945.4 333461 . N . . . . GT ./. NC_002945.4 333462 . N . . . . GT ./. NC_002945.4 333463 . N . . . . GT ./. NC_002945.4 333464 . N . . . . GT ./. NC_002945.4 333465 . N . . . . GT ./. NC_002945.4 333466 . N . . . . GT ./. NC_002945.4 333467 . N . . . . GT ./. NC_002945.4 333468 . N . . . . GT ./. NC_002945.4 333469 . N . . . . GT ./. NC_002945.4 333470 . N . . . . GT ./. NC_002945.4 334320 . T C 4403.03 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=158;CIGAR=1X;DP=161;DPB=161;DPRA=0;EPP=3.88988;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQ=52.481;MQMR=39;NS=1;NUMALT=1;ODDS=205.555;PAIRED=0.987342;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=5203;QR=70;RO=2;RPL=71;RPP=6.52863;RPPR=7.35324;RPR=87;RUN=1;SAF=84;SAP=4.38465;SAR=74;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:161:2,158:2:70:158:5203:-443.268,-42.0072,0 NC_002945.4 336585 . N . . . . GT ./. NC_002945.4 336586 . N . . . . GT ./. NC_002945.4 336587 . N . . . . GT ./. NC_002945.4 336588 . N . . . . GT ./. NC_002945.4 336589 . N . . . . GT ./. NC_002945.4 336590 . N . . . . GT ./. NC_002945.4 336591 . N . . . . GT ./. NC_002945.4 336592 . N . . . . GT ./. NC_002945.4 336593 . N . . . . GT ./. NC_002945.4 336594 . N . . . . GT ./. NC_002945.4 336595 . N . . . . GT ./. NC_002945.4 340088 . G A 5406.05 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=169;CIGAR=1X;DP=170;DPB=170;DPRA=0;EPP=4.05106;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=59.503;MQMR=0;NS=1;NUMALT=1;ODDS=238.889;PAIRED=0.994083;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6099;QR=0;RO=0;RPL=58;RPP=39.103;RPPR=0;RPR=111;RUN=1;SAF=89;SAP=4.05106;SAR=80;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:170:0,169:0:0:169:6099:-548.098,-50.8741,0 NC_002945.4 624554 . N . . . . GT ./. NC_002945.4 624555 . N . . . . GT ./. NC_002945.4 624556 . N . . . . GT ./. NC_002945.4 624557 . N . . . . GT ./. NC_002945.4 624558 . N . . . . GT ./. NC_002945.4 624559 . N . . . . GT ./. NC_002945.4 624560 . N . . . . GT ./. NC_002945.4 624561 . N . . . . GT ./. NC_002945.4 624562 . N . . . . GT ./. NC_002945.4 624563 . N . . . . GT ./. NC_002945.4 641896 . A C 6646.66 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=217;CIGAR=1X;DP=217;DPB=217;DPRA=0;EPP=5.26183;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=305.431;PAIRED=0.990783;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7442;QR=0;RO=0;RPL=94;RPP=11.426;RPPR=0;RPR=123;RUN=1;SAF=101;SAP=5.26183;SAR=116;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:217:0,217:0:0:217:7442:-669.755,-65.3235,0