annotate test-data/SRR1792272_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/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