annotate test-data/SRR8073662_zc.vcf @ 13:cd636b0e4f95 draft

"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"

##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