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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76-dirty
| author | sanbi-uwc |
|---|---|
| date | Wed, 17 Oct 2018 02:35:51 -0400 |
| parents | f58178c0f00d |
| children |
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##fileformat=VCFv4.1 ##fileDate=20170123 ##source=freeBayes v0.9.20 ##reference=localref.fa ##phasing=none ##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15535.dat" ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus"> ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype"> ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes"> ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]"> ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally"> ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally"> ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally"> ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally"> ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred"> ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred"> ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations"> ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations"> ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand"> ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand"> ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand"> ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand"> ##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous"> ##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome"> ##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele"> ##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele"> ##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality"> ##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio. Ratio between depth in samples with each called alternate allele and those without."> ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best."> ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout."> ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex."> ##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing. Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR."> ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position."> ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles."> ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length"> ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles"> ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles"> ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments"> ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments"> ##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=GQ,Number=1,Type=Float,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=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"> ##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani" ##SnpEffCmd="SnpEff -i vcf -o vcf -stats /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15558.dat m_tuberculosis_H37Rv /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15535.dat " ##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO' "> ##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 FORMAT $i NC_000962 1849 . C A 10026.9 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=361;CIGAR=1X;DP=362;DPB=362;DPRA=0;EPP=17.4527;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=491.444;PAIRED=0.972299;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=11220;QR=23;RO=1;RPL=173;RPP=4.36371;RPPR=5.18177;RPR=188;RUN=1;SAF=169;SAP=6.19232;SAR=192;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:362:1:23:361:11220:-1007.81,-104.114,0 NC_000962 1977 . A G 5808.79 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=206;CIGAR=1X;DP=206;DPB=206;DPRA=0;EPP=4.06441;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=290.182;PAIRED=0.995146;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6612;QR=0;RO=0;RPL=82;RPP=21.6049;RPPR=0;RPR=124;RUN=1;SAF=58;SAP=88.3934;SAR=148;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:206:0:0:206:6612:-595.401,-62.0122,0 NC_000962 4013 . T C 7210.29 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=240;CIGAR=1X;DP=240;DPB=240;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=337.316;PAIRED=0.991667;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8059;QR=0;RO=0;RPL=132;RPP=8.22183;RPPR=0;RPR=108;RUN=1;SAF=128;SAP=5.32654;SAR=112;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:240:0:0:240:8059:-725.646,-72.2472,0 NC_000962 7362 . G C 6381.78 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=216;CIGAR=1X;DP=216;DPB=216;DPRA=0;EPP=6.26751;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=304.045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7135;QR=0;RO=0;RPL=114;RPP=4.45795;RPPR=0;RPR=102;RUN=1;SAF=111;SAP=3.37221;SAR=105;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:216:0:0:216:7135:-642.48,-65.0225,0 NC_000962 7585 . G C 5383.07 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=184;CIGAR=1X;DP=184;DPB=184;DPRA=0;EPP=10.9881;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.5761;MQMR=0;NS=1;NUMALT=1;ODDS=259.683;PAIRED=0.98913;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6035;QR=0;RO=0;RPL=101;RPP=6.83398;RPPR=0;RPR=83;RUN=1;SAF=100;SAP=6.03148;SAR=84;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:184:0:0:184:6035:-543.478,-55.3895,0 NC_000962 9304 . G A 4335.96 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=168;CIGAR=1X;DP=168;DPB=168;DPRA=0;EPP=5.54368;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=237.503;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4866;QR=0;RO=0;RPL=96;RPP=10.4553;RPPR=0;RPR=72;RUN=1;SAF=85;SAP=3.062;SAR=83;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:168:0:0:168:4866:-438.23,-50.573,0 NC_000962 11820 . C G 6752.81 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=225;CIGAR=1X;DP=226;DPB=226;DPRA=0;EPP=3.25157;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=301.087;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7623;QR=35;RO=1;RPL=139;RPP=30.1199;RPPR=5.18177;RPR=86;RUN=1;SAF=90;SAP=22.5536;SAR=135;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:226:1:35:225:7623:-682.909,-62.1787,0 NC_000962 11879 . A G 5087.99 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=168;CIGAR=1X;DP=169;DPB=169;DPRA=0;EPP=6.31921;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=237.503;PAIRED=0.988095;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5696;QR=0;RO=0;RPL=88;RPP=3.83753;RPPR=0;RPR=80;RUN=1;SAF=80;SAP=3.83753;SAR=88;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:169:0:0:168:5696:-512.927,-50.573,0 NC_000962 14785 . T C 8206.81 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=271;CIGAR=1X;DP=271;DPB=271;DPRA=0;EPP=15.1978;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=380.291;PAIRED=0.99262;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9193;QR=0;RO=0;RPL=120;RPP=10.7106;RPPR=0;RPR=151;RUN=1;SAF=117;SAP=13.9798;SAR=154;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:271:0:0:271:9193:-827.709,-81.5791,0 NC_000962 14861 . G T 6584.26 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=248;CIGAR=1X;DP=250;DPB=250;DPRA=0;EPP=4.72646;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=339.467;PAIRED=0.995968;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7384;QR=7;RO=1;RPL=147;RPP=21.5379;RPPR=5.18177;RPR=101;RUN=1;SAF=138;SAP=9.87495;SAR=110;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:250:1:7:248:7384:-664.122,-71.9653,0 NC_000962 15117 . C G 7023.86 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=236;CIGAR=1X;DP=236;DPB=236;DPRA=0;EPP=12.4323;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=331.771;PAIRED=0.995763;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7856;QR=0;RO=0;RPL=122;RPP=3.59917;RPPR=0;RPR=114;RUN=1;SAF=112;SAP=4.33527;SAR=124;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:236:0:0:236:7856:-707.373,-71.0431,0 NC_000962 16119 . C A 5448.86 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=205;CIGAR=1X;DP=205;DPB=205;DPRA=0;EPP=3.27511;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=288.796;PAIRED=0.990244;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6115;QR=0;RO=0;RPL=104;RPP=3.10563;RPPR=0;RPR=101;RUN=1;SAF=81;SAP=22.5959;SAR=124;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:205:0:0:205:6115:-550.648,-61.7111,0 NC_000962 21795 . G A 2468.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=96;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=137.689;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2785;QR=0;RO=0;RPL=51;RPP=3.8246;RPPR=0;RPR=45;RUN=1;SAF=39;SAP=10.339;SAR=57;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:96:0:0:96:2785:-250.94,-28.8989,0 NC_000962 24698 . GCCGCGTTGCTCGGGGTAAC GC 1897.42 . AB=0.782946;ABP=92.714;AC=1;AF=0.5;AN=2;AO=101;CIGAR=1M18D1M;DP=129;DPB=56.3;DPRA=0;EPP=4.75178;EPPR=10.7656;GTI=0;LEN=18;MEANALT=1;MQM=74.0297;MQMR=68.3571;NS=1;NUMALT=1;ODDS=104.859;PAIRED=1;PAIREDR=1;PAO=3;PQA=67;PQR=1057;PRO=34;QA=2503;QR=870;RO=28;RPL=19;RPP=88.3427;RPPR=55.4358;RPR=82;RUN=1;SAF=52;SAP=3.2038;SAR=49;SRF=18;SRP=7.97367;SRR=10;TYPE=del;technology.ILLUMINA=1;ANN=GC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 0/1:129:28:870:101:2503:-214.923,0,-68.0161 NC_000962 25610 . G C 5995.34 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=203;CIGAR=1X;DP=203;DPB=203;DPRA=0;EPP=45.4663;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=286.023;PAIRED=0.990148;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6847;QR=0;RO=0;RPL=61;RPP=73.1927;RPPR=0;RPR=142;RUN=1;SAF=81;SAP=20.9918;SAR=122;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:203:0:0:203:6847:-616.567,-61.1091,0 NC_000962 26959 . C G 4810.71 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=167;CIGAR=1X;DP=168;DPB=168;DPRA=0;EPP=20.8112;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=236.116;PAIRED=0.988024;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5426;QR=0;RO=0;RPL=65;RPP=20.8112;RPPR=0;RPR=102;RUN=1;SAF=92;SAP=6.76812;SAR=75;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:168:0:0:167:5426:-488.643,-50.272,0 NC_000962 28366 . ATT AT 4035.74 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=157;CIGAR=1M1D1M;DP=157;DPB=110;DPRA=0;EPP=4.13061;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=222.253;PAIRED=0.980892;PAIREDR=0;PAO=6;PQA=115.5;PQR=115.5;PRO=6;QA=4550;QR=0;RO=0;RPL=62;RPP=18.0723;RPPR=0;RPR=95;RUN=1;SAF=65;SAP=13.0931;SAR=92;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=AT||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:4550:-409.79,-47.2617,0 NC_000962 34044 . T C 7774.47 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=260;CIGAR=1X;DP=261;DPB=261;DPRA=0;EPP=3.14393;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=365.042;PAIRED=0.996154;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8695;QR=0;RO=0;RPL=149;RPP=15.0703;RPPR=0;RPR=111;RUN=1;SAF=121;SAP=5.71629;SAR=139;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:261:0:0:260:8695:-782.853,-78.2678,0 NC_000962 35608 . C T 6319.96 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=239;CIGAR=1X;DP=239;DPB=239;DPRA=0;EPP=4.10966;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.9079;MQMR=0;NS=1;NUMALT=1;ODDS=335.93;PAIRED=0.991632;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7067;QR=0;RO=0;RPL=126;RPP=4.54578;RPPR=0;RPR=113;RUN=1;SAF=112;SAP=5.05457;SAR=127;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:239:0:0:239:7067:-636.326,-71.9462,0 NC_000962 36008 . G C 3949.86 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=133;CIGAR=1X;DP=134;DPB=134;DPRA=0;EPP=3.81032;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=177.817;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4444;QR=21;RO=1;RPL=75;RPP=7.72876;RPPR=5.18177;RPR=58;RUN=1;SAF=63;SAP=3.81032;SAR=70;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:134:1:21:133:4444:-398.194,-36.1109,0 NC_000962 36209 . T C 3333.09 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=114;CIGAR=1X;DP=115;DPB=115;DPRA=0;EPP=3.69603;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=162.643;PAIRED=0.991228;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3766;QR=0;RO=0;RPL=57;RPP=3.0103;RPPR=0;RPR=57;RUN=1;SAF=75;SAP=27.6965;SAR=39;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:115:0:0:114:3766:-339.248,-34.3174,0 NC_000962 37031 . C G 5160.39 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=178;CIGAR=1X;DP=178;DPB=178;DPRA=0;EPP=4.23023;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=251.366;PAIRED=0.988764;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5775;QR=0;RO=0;RPL=90;RPP=3.0591;RPPR=0;RPR=88;RUN=1;SAF=96;SAP=5.40136;SAR=82;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:178:0:0:178:5775:-520.074,-53.5833,0 NC_000962 37305 . C G 5497.25 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=184;CIGAR=1X;DP=184;DPB=184;DPRA=0;EPP=6.83398;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=259.683;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6153;QR=0;RO=0;RPL=91;RPP=3.05751;RPPR=0;RPR=93;RUN=1;SAF=84;SAP=6.03148;SAR=100;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:184:0:0:184:6153:-554.104,-55.3895,0 NC_000962 39030 . C T 15330.8 . AB=0.801205;ABP=657.068;AC=1;AF=0.5;AN=2;AO=665;CIGAR=1X;DP=830;DPB=830;DPRA=0;EPP=127.176;EPPR=14.0782;GTI=0;LEN=1;MEANALT=1;MQM=68.1218;MQMR=68.0606;NS=1;NUMALT=1;ODDS=667.945;PAIRED=0.969925;PAIREDR=0.939394;PAO=0;PQA=0;PQR=0;PRO=0;QA=19384;QR=4913;RO=165;RPL=514;RPP=433.285;RPPR=19.1318;RPR=151;RUN=1;SAF=276;SAP=44.7058;SAR=389;SRF=69;SRP=12.6043;SRR=96;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 0/1:830:165:4913:665:19384:-1673.31,0,-370.926 NC_000962 39158 . C G 5416.98 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=179;CIGAR=1X;DP=179;DPB=179;DPRA=0;EPP=4.47817;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.4693;MQMR=0;NS=1;NUMALT=1;ODDS=252.752;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6069;QR=0;RO=0;RPL=91;RPP=3.11948;RPPR=0;RPR=88;RUN=1;SAF=104;SAP=13.2126;SAR=75;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:179:0:0:179:6069:-546.549,-53.8844,0 NC_000962 42281 . C A 3862.85 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=148;CIGAR=1X;DP=148;DPB=148;DPRA=0;EPP=5.12308;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.8649;MQMR=0;NS=1;NUMALT=1;ODDS=209.777;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4341;QR=0;RO=0;RPL=78;RPP=3.94932;RPPR=0;RPR=70;RUN=1;SAF=62;SAP=11.4614;SAR=86;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:148:0:0:148:4341:-390.983,-44.5524,0 NC_000962 42967 . G C 4783.78 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=165;CIGAR=1X;DP=165;DPB=165;DPRA=0;EPP=9.97217;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=233.344;PAIRED=0.993939;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5476;QR=0;RO=0;RPL=79;RPP=3.65516;RPPR=0;RPR=86;RUN=1;SAF=39;SAP=102.622;SAR=126;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:165:0:0:165:5476:-493.172,-49.6699,0 NC_000962 44768 . A G 5762.88 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=192;CIGAR=1X;DP=192;DPB=192;DPRA=0;EPP=14.5915;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=270.774;PAIRED=0.994792;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6474;QR=0;RO=0;RPL=76;RPP=21.1059;RPPR=0;RPR=116;RUN=1;SAF=94;SAP=3.19126;SAR=98;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:192:0:0:192:6474:-582.997,-57.7978,0 NC_000962 48347 . G A 4144.13 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=157;CIGAR=1X;DP=157;DPB=157;DPRA=0;EPP=5.34774;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=222.253;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4646;QR=0;RO=0;RPL=84;RPP=4.68386;RPPR=0;RPR=73;RUN=1;SAF=81;SAP=3.35608;SAR=76;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:157:0:0:157:4646:-418.436,-47.2617,0 NC_000962 49360 . C T 4289.47 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=163;CIGAR=1X;DP=163;DPB=163;DPRA=0;EPP=3.02362;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.9632;MQMR=0;NS=1;NUMALT=1;ODDS=230.571;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4818;QR=0;RO=0;RPL=90;RPP=6.86033;RPPR=0;RPR=73;RUN=1;SAF=68;SAP=12.722;SAR=95;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:163:0:0:163:4818:-433.916,-49.0679,0 NC_000962 49690 . GCCC GC 4384.5 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=172;CIGAR=1M2D1M;DP=172;DPB=96.5;DPRA=0;EPP=4.27278;EPPR=0;GTI=0;LEN=2;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=243.048;PAIRED=1;PAIREDR=0;PAO=14;PQA=389.5;PQR=389.5;PRO=14;QA=4933;QR=0;RO=0;RPL=85;RPP=3.0608;RPPR=0;RPR=87;RUN=1;SAF=106;SAP=23.21;SAR=66;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=GC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:172:0:0:172:4933:-444.257,-51.7772,0 NC_000962 50557 . T C 6353.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=215;CIGAR=1X;DP=215;DPB=215;DPRA=0;EPP=15.3826;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.907;MQMR=0;NS=1;NUMALT=1;ODDS=302.658;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7114;QR=0;RO=0;RPL=101;RPP=4.71718;RPPR=0;RPR=114;RUN=1;SAF=104;SAP=3.50519;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:215:0:0:215:7114:-640.591,-64.7214,0 NC_000962 51949 . A G 7366.08 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=248;CIGAR=1X;DP=248;DPB=248;DPRA=0;EPP=6.51267;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=348.406;PAIRED=0.995968;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8237;QR=0;RO=0;RPL=121;RPP=3.32551;RPPR=0;RPR=127;RUN=1;SAF=109;SAP=10.8906;SAR=139;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:248:0:0:248:8237:-741.662,-74.6554,0 NC_000962 54394 . A G 5742.65 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=192;CIGAR=1X;DP=193;DPB=193;DPRA=0;EPP=4.6389;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=270.774;PAIRED=0.994792;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6423;QR=0;RO=0;RPL=89;RPP=5.22701;RPPR=0;RPR=103;RUN=1;SAF=95;SAP=3.05554;SAR=97;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:193:0:0:192:6423:-578.373,-57.7978,0 NC_000962 55543 . GC GCCGCCTCCAC 1414.15 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=72;CIGAR=1M9I1M;DP=77;DPB=435;DPRA=0;EPP=4.9405;EPPR=3.73412;GTI=0;LEN=9;MEANALT=3;MQM=71.25;MQMR=70;NS=1;NUMALT=1;ODDS=72.5878;PAIRED=1;PAIREDR=1;PAO=12;PQA=103;PQR=34;PRO=7;QA=1709;QR=80;RO=3;RPL=34;RPP=3.49285;RPPR=3.73412;RPR=38;RUN=1;SAF=20;SAP=33.8935;SAR=52;SRF=1;SRP=3.73412;SRR=2;TYPE=ins;technology.ILLUMINA=1;ANN=GCCGCCTCCAC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:77:3:80:72:1709:-146.612,-10.4988,0 NC_000962 55553 . C T 2864.98 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=117;CIGAR=1X;DP=117;DPB=117;DPRA=0;EPP=11.1951;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70.9402;MQMR=0;NS=1;NUMALT=1;ODDS=166.802;PAIRED=0.991453;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3329;QR=0;RO=0;RPL=32;RPP=55.1442;RPPR=0;RPR=85;RUN=1;SAF=36;SAP=40.5935;SAR=81;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:117:0:0:117:3329:-299.895,-35.2205,0 NC_000962 62049 . A G 3935.57 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=138;CIGAR=1X;DP=139;DPB=139;DPRA=0;EPP=9.30442;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=195.914;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4458;QR=0;RO=0;RPL=74;RPP=4.58383;RPPR=0;RPR=64;RUN=1;SAF=93;SAP=39.2644;SAR=45;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:139:0:0:138:4458:-401.521,-41.5421,0 NC_000962 63146 . G T 8455.87 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=308;CIGAR=1X;DP=308;DPB=308;DPRA=0;EPP=4.02553;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=431.584;PAIRED=0.996753;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=9456;QR=0;RO=0;RPL=161;RPP=4.39215;RPPR=0;RPR=147;RUN=1;SAF=131;SAP=17.9286;SAR=177;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:308:0:0:308:9456:-851.347,-92.7172,0 NC_000962 65150 . C T 6774.69 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=253;CIGAR=1X;DP=256;DPB=256;DPRA=0;EPP=3.22487;EPPR=3.0103;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=330.472;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7606;QR=45;RO=2;RPL=122;RPP=3.70551;RPPR=3.0103;RPR=131;RUN=1;SAF=137;SAP=6.79536;SAR=116;SRF=2;SRP=7.35324;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:256:2:45:253:7606:-680.633,-68.0656,0 NC_000962 66248 . C T 4586.61 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=167;CIGAR=1X;DP=167;DPB=167;DPRA=0;EPP=13.9457;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=69.8743;MQMR=0;NS=1;NUMALT=1;ODDS=236.116;PAIRED=0.988024;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5146;QR=0;RO=0;RPL=80;RPP=3.64744;RPPR=0;RPR=87;RUN=1;SAF=84;SAP=3.0233;SAR=83;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:167:0:0:167:5146:-463.448,-50.272,0 NC_000962 68337 . TCA TCCA 6836.5 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=260;CIGAR=1M1I2M;DP=261;DPB=353.333;DPRA=0;EPP=3.04371;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=350.471;PAIRED=0.996154;PAIREDR=1;PAO=6;PQA=175;PQR=175;PRO=6;QA=7667;QR=30;RO=1;RPL=129;RPP=3.04371;RPPR=5.18177;RPR=131;RUN=1;SAF=144;SAP=9.55812;SAR=116;SRF=0;SRP=5.18177;SRR=1;TYPE=ins;technology.ILLUMINA=1;ANN=TCCA||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:261:1:30:260:7667:-687.325,-73.1522,0