Mercurial > repos > iuc > vsnp_determine_ref_from_data
view test-data/SRR8073662_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/SRR8073662/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/SRR8073662/NC_002945v4.fasta /scratch/analysis_staging/a_script/vcf_test_files_sra_downloaded_2019-01-23/SRR8073662/SRR8073662-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 SRR8073662 NC_002945.4 1057 . A G 1991.37 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=78;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=4.01252;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=112.736;PAIRED=0.961538;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2256;QR=0;RO=0;RPL=41;RPP=3.45573;RPPR=0;RPR=37;RUN=1;SAF=47;SAP=10.1372;SAR=31;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:80:0,78:0:0:78:2256:-203.125,-23.4803,0 NC_002945.4 29470 . N . . . . GT ./. 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 33788 . A G 1024.83 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=3.22745;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=60.0569;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1290;QR=0;RO=0;RPL=21;RPP=3.22745;RPPR=0;RPR=19;RUN=1;SAF=40;SAP=89.8692;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:40:0,40:0:0:40:1290:-116.37,-12.0412,0 NC_002945.4 132052 . N . . . . GT ./. NC_002945.4 132620 . N . . . . GT ./. NC_002945.4 132621 . N . . . . GT ./. NC_002945.4 132622 . N . . . . GT ./. NC_002945.4 132623 . N . . . . GT ./. NC_002945.4 132624 . N . . . . GT ./. NC_002945.4 132625 . N . . . . GT ./. NC_002945.4 132626 . N . . . . GT ./. NC_002945.4 132627 . N . . . . GT ./. NC_002945.4 132628 . N . . . . GT ./. NC_002945.4 132629 . N . . . . GT ./. NC_002945.4 140686 . A G 2969.95 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=110;CIGAR=1X;DP=112;DPB=112;DPRA=0;EPP=4.2737;EPPR=0;GTI=0;LEN=1;MEANALT=3;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=157.098;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3362;QR=0;RO=0;RPL=71;RPP=23.2247;RPPR=0;RPR=39;RUN=1;SAF=52;SAP=3.72096;SAR=58;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:112:0,110:0:0:110:3362:-302.582,-33.1133,0 NC_002945.4 149955 . N . . . . GT ./. NC_002945.4 149956 . N . . . . GT ./. NC_002945.4 149957 . N . . . . GT ./. NC_002945.4 149958 . N . . . . GT ./. NC_002945.4 149959 . N . . . . GT ./. NC_002945.4 149960 . N . . . . GT ./. NC_002945.4 149961 . N . . . . GT ./. NC_002945.4 149962 . N . . . . GT ./. NC_002945.4 149963 . N . . . . GT ./. NC_002945.4 149964 . N . . . . GT ./. NC_002945.4 160535 . T C 1804.25 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=74;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=3.12768;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQ=59.8649;MQMR=60;NS=1;NUMALT=1;ODDS=100.699;PAIRED=0.986486;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2050;QR=25;RO=2;RPL=41;RPP=4.88833;RPPR=7.35324;RPR=33;RUN=1;SAF=31;SAP=7.23587;SAR=43;SRF=2;SRP=7.35324;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:76:2,74:2:25:74:2050:-182.337,-20.5033,0 NC_002945.4 306688 . N . . . . GT ./. NC_002945.4 306689 . N . . . . GT ./. NC_002945.4 306690 . N . . . . GT ./. NC_002945.4 306691 . N . . . . GT ./. NC_002945.4 306692 . N . . . . GT ./. NC_002945.4 306693 . N . . . . GT ./. NC_002945.4 306694 . N . . . . GT ./. NC_002945.4 306695 . N . . . . GT ./. NC_002945.4 306696 . N . . . . GT ./. NC_002945.4 306697 . N . . . . GT ./. NC_002945.4 319911 . C T 1185.93 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=43;CIGAR=1X;DP=43;DPB=43;DPRA=0;EPP=3.0608;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQ=60;MQMR=0;NS=1;NUMALT=1;ODDS=64.2158;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1346;QR=0;RO=0;RPL=20;RPP=3.46479;RPPR=0;RPR=23;RUN=1;SAF=22;SAP=3.0608;SAR=21;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1 GT:DP:AD:RO:QR:AO:QA:GL 1/1:43:0,43:0:0:43:1346:-121.399,-12.9443,0