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annotate test-data/vcf2.vcf @ 5:4f3f7d390382 draft default tip

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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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cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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1 ##fileformat=VCFv4.1
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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2 ##fileDate=20170123
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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3 ##source=freeBayes v0.9.20
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4 ##reference=localref.fa
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5 ##phasing=none
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6 ##commandline="freebayes --bam localbam_0.bam --fasta-reference localref.fa --vcf /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15534.dat"
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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7 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
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8 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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9 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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10 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
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11 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
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12 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
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13 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
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14 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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15 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
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16 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
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17 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
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18 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
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19 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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20 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
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21 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
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22 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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23 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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24 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
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25 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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26 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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27 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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28 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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29 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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30 ##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">
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31 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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32 ##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">
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33 ##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">
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34 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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35 ##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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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36 ##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.">
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37 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
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38 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
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39 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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40 ##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.">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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41 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
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42 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
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43 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
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44 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
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45 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
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46 ##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
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47 ##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
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48 ##INFO=<ID=technology.ILLUMINA,Number=A,Type=Float,Description="Fraction of observations supporting the alternate observed in reads from ILLUMINA">
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49 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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50 ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
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51 ##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">
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52 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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53 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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54 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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55 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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56 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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57 ##SnpEffVersion="4.1l (build 2015-10-03), by Pablo Cingolani"
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58 ##SnpEffCmd="SnpEff -i vcf -o vcf -stats /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15556.dat m_tuberculosis_H37Rv /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15534.dat "
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59 ##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' ">
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60 ##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' ">
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61 ##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' ">
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62 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $i
4
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63 NC_000962 1977 . A G 2997.91 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=99;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=10.9285;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=141.848;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3410;QR=0;RO=0;RPL=39;RPP=12.6832;RPPR=0;RPR=60;RUN=1;SAF=33;SAP=26.8965;SAR=66;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 1/1:99:0:0:99:3410:-307.244,-29.802,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
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64 NC_000962 4013 . T C 2774.81 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=88;CIGAR=1X;DP=88;DPB=88;DPRA=0;EPP=3.89863;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=126.599;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3137;QR=0;RO=0;RPL=51;RPP=7.84676;RPPR=0;RPR=37;RUN=1;SAF=56;SAP=17.2236;SAR=32;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 1/1:88:0:0:88:3137:-282.686,-26.4906,0
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diff changeset
65 NC_000962 6608 . G C 4499.46 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=147;CIGAR=1X;DP=149;DPB=149;DPRA=0;EPP=3.02507;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=180.956;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=5103;QR=72;RO=2;RPL=60;RPP=13.779;RPPR=7.35324;RPR=87;RUN=1;SAF=72;SAP=3.14325;SAR=75;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:149:2:72:147:5103:-452.777,-33.9711,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
66 NC_000962 7362 . G C 2651.87 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=85;CIGAR=1X;DP=85;DPB=85;DPRA=0;EPP=5.07959;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=122.44;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2982;QR=0;RO=0;RPL=44;RPP=3.24022;RPPR=0;RPR=41;RUN=1;SAF=39;SAP=4.26209;SAR=46;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 1/1:85:0:0:85:2982:-268.731,-25.5875,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
67 NC_000962 7585 . G C 2367.43 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=76;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=3.12459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=109.964;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2662;QR=0;RO=0;RPL=36;RPP=3.46745;RPPR=0;RPR=40;RUN=1;SAF=37;SAP=3.12459;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 1/1:76:0:0:76:2662:-239.93,-22.8783,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
68 NC_000962 9304 . G A 2662.92 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=98;CIGAR=1X;DP=98;DPB=98;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=140.462;PAIRED=0.989796;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3000;QR=0;RO=0;RPL=54;RPP=5.22609;RPPR=0;RPR=44;RUN=1;SAF=46;SAP=3.80798;SAR=52;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 1/1:98:0:0:98:3000:-270.306,-29.5009,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
69 NC_000962 11370 . C T 3624.69 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=132;CIGAR=1X;DP=133;DPB=133;DPRA=0;EPP=3.0761;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=172.992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4105;QR=36;RO=1;RPL=66;RPP=3.0103;RPPR=5.18177;RPR=66;RUN=1;SAF=53;SAP=14.1309;SAR=79;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:133:1:36:132:4105:-366.161,-34.3131,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
70 NC_000962 11879 . A G 2391.08 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=76;CIGAR=1X;DP=76;DPB=76;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=109.964;PAIRED=0.986842;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2690;QR=0;RO=0;RPL=42;RPP=4.83891;RPPR=0;RPR=34;RUN=1;SAF=36;SAP=3.46745;SAR=40;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 1/1:76:0:0:76:2690:-242.454,-22.8783,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
71 NC_000962 14785 . T C 3096.22 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=99;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=4.78696;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=141.848;PAIRED=0.979798;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3478;QR=0;RO=0;RPL=54;RPP=4.78696;RPPR=0;RPR=45;RUN=1;SAF=46;SAP=4.08507;SAR=53;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 1/1:99:0:0:99:3478:-313.371,-29.802,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
72 NC_000962 21795 . G A 1207.06 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=47;CIGAR=1X;DP=47;DPB=47;DPRA=0;EPP=5.27418;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=69.761;PAIRED=0.978723;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1379;QR=0;RO=0;RPL=29;RPP=8.60069;RPPR=0;RPR=18;RUN=1;SAF=26;SAP=4.16534;SAR=21;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 1/1:47:0:0:47:1379:-124.403,-14.1484,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
73 NC_000962 24698 . GCCGCGTTGCTCGGGGTAAC GC 1057.11 . AB=0.787879;ABP=50.5195;AC=1;AF=0.5;AN=2;AO=52;CIGAR=1M18D1M;DP=66;DPB=23.95;DPRA=0;EPP=9.02361;EPPR=3.17734;GTI=0;LEN=18;MEANALT=2;MQM=72.0962;MQMR=70;NS=1;NUMALT=1;ODDS=41.6884;PAIRED=0.961538;PAIREDR=1;PAO=2;PQA=54.5;PQR=359.5;PRO=11;QA=1422;QR=421;RO=13;RPL=13;RPP=31.2394;RPPR=31.2394;RPR=39;RUN=1;SAF=35;SAP=16.5402;SAR=17;SRF=7;SRP=3.17734;SRR=6;TYPE=del;technology.ILLUMINA=1;ANN=GC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 0/1:66:13:421:52:1422:-121.779,0,-31.7277
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
74 NC_000962 26959 . C G 2762.4 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=92;CIGAR=1X;DP=92;DPB=92;DPRA=0;EPP=37.093;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=132.144;PAIRED=0.98913;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3144;QR=0;RO=0;RPL=40;RPP=6.40913;RPPR=0;RPR=52;RUN=1;SAF=45;SAP=3.10471;SAR=47;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 1/1:92:0:0:92:3144:-283.302,-27.6948,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
75 NC_000962 27141 . C G 2038.01 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=67;CIGAR=1X;DP=67;DPB=67;DPRA=0;EPP=3.04271;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=97.4869;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2318;QR=0;RO=0;RPL=46;RPP=23.2666;RPPR=0;RPR=21;RUN=1;SAF=36;SAP=3.82055;SAR=31;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 1/1:67:0:0:67:2318:-208.966,-20.169,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
76 NC_000962 28532 . C G 2110.66 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=71;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=3.7749;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=78.4659;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2450;QR=72;RO=2;RPL=46;RPP=16.4979;RPPR=7.35324;RPR=25;RUN=1;SAF=40;SAP=5.48761;SAR=31;SRF=2;SRP=7.35324;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:73:2:72:71:2450:-214.005,-11.7156,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
77 NC_000962 29482 . CAA CA 2283.56 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=87;CIGAR=1M1D1M;DP=90;DPB=63;DPRA=0;EPP=10.2236;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=89.4336;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=63;PQR=63;PRO=2.5;QA=2664;QR=96;RO=3;RPL=51;RPP=8.62618;RPPR=3.73412;RPR=36;RUN=1;SAF=45;SAP=3.23494;SAR=42;SRF=0;SRP=9.52472;SRR=3;TYPE=del;technology.ILLUMINA=1;ANN=CA||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:90:3:96:87:2664:-231.106,-13.0627,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
78 NC_000962 30519 . C T 2239.24 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=84;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=3.94093;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=121.054;PAIRED=0.988095;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2546;QR=0;RO=0;RPL=56;RPP=23.2774;RPPR=0;RPR=28;RUN=1;SAF=45;SAP=3.94093;SAR=39;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 1/1:86:0:0:84:2546:-229.333,-25.2865,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
79 NC_000962 30688 . T G 2477.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=81;CIGAR=1X;DP=81;DPB=81;DPRA=0;EPP=7.5409;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=116.895;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2793;QR=0;RO=0;RPL=46;RPP=6.2541;RPPR=0;RPR=35;RUN=1;SAF=39;SAP=3.25157;SAR=42;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 1/1:81:0:0:81:2793:-251.715,-24.3834,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
80 NC_000962 30943 . C T 1995.15 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=79;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=20.1897;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=114.122;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2278;QR=0;RO=0;RPL=43;RPP=4.35716;RPPR=0;RPR=36;RUN=1;SAF=48;SAP=10.954;SAR=31;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 1/1:79:0:0:79:2278:-205.308,-23.7814,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
81 NC_000962 31077 . C T 2093.17 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=80;CIGAR=1X;DP=81;DPB=81;DPRA=0;EPP=4.74748;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=102.127;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2393;QR=35;RO=1;RPL=34;RPP=6.91895;RPPR=5.18177;RPR=46;RUN=1;SAF=42;SAP=3.44459;SAR=38;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.ILLUMINA=1;ANN=T||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:81:1:35:80:2393:-212.169,-18.9749,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
82 NC_000962 32349 . CCCGCGCGTCGGCGATGCGTCGCGTCGAGTCGGCGATGC CC 452.327 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1M37D1M;DP=22;DPB=2.94872;DPRA=0;EPP=6.56362;EPPR=0;GTI=0;LEN=37;MEANALT=1;MQM=52.5455;MQMR=0;NS=1;NUMALT=1;ODDS=35.1036;PAIRED=1;PAIREDR=0;PAO=19;PQA=637;PQR=637;PRO=19;QA=547;QR=0;RO=0;RPL=17;RPP=17.2236;RPPR=0;RPR=5;RUN=1;SAF=9;SAP=4.58955;SAR=13;SRF=0;SRP=0;SRR=0;TYPE=del;technology.ILLUMINA=1;ANN=CC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:547:-49.4786,-6.62266,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
83 NC_000962 34044 . T C 3715.45 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=119;CIGAR=1X;DP=119;DPB=119;DPRA=0;EPP=8.28388;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=169.574;PAIRED=0.991597;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4178;QR=0;RO=0;RPL=63;RPP=3.90444;RPPR=0;RPR=56;RUN=1;SAF=70;SAP=11.0575;SAR=49;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 1/1:119:0:0:119:4178:-376.371,-35.8226,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
84 NC_000962 37031 . C G 2680.99 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=87;CIGAR=1X;DP=87;DPB=87;DPRA=0;EPP=6.03039;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=125.213;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3018;QR=0;RO=0;RPL=46;RPP=3.63429;RPPR=0;RPR=41;RUN=1;SAF=38;SAP=6.03039;SAR=49;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 1/1:87:0:0:87:3018:-271.967,-26.1896,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
85 NC_000962 42967 . G C 2729.44 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=88;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=119.936;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=3105;QR=5;RO=1;RPL=44;RPP=3.0103;RPPR=5.18177;RPR=44;RUN=1;SAF=24;SAP=42.4916;SAR=64;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=C||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:89:1:5:88:3105:-279.303,-24.3423,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
86 NC_000962 50557 . T C 3706.43 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=117;CIGAR=1X;DP=117;DPB=117;DPRA=0;EPP=3.91972;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=166.802;PAIRED=0.991453;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4160;QR=0;RO=0;RPL=52;RPP=6.14687;RPPR=0;RPR=65;RUN=1;SAF=52;SAP=6.14687;SAR=65;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 1/1:117:0:0:117:4160:-374.756,-35.2205,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
87 NC_000962 51949 . A G 3926.12 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=127;CIGAR=1X;DP=129;DPB=129;DPRA=0;EPP=5.8999;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=154.829;PAIRED=0.992126;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4487;QR=61;RO=2;RPL=66;RPP=3.43776;RPPR=3.0103;RPR=61;RUN=1;SAF=42;SAP=34.6249;SAR=85;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:129:2:61:127:4487:-398.388,-29.1211,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
88 NC_000962 51954 . T A 3348.08 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=125;CIGAR=1X;DP=127;DPB=127;DPRA=0;EPP=3.02767;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=152.119;PAIRED=0.992;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=3828;QR=61;RO=2;RPL=66;RPP=3.86152;RPPR=3.0103;RPR=59;RUN=1;SAF=46;SAP=21.9282;SAR=79;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=A||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:127:2:61:125:3828:-339.031,-28.5327,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
89 NC_000962 53785 . C G 3902.21 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=127;CIGAR=1X;DP=130;DPB=130;DPRA=0;EPP=19.4417;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=140.055;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4493;QR=103;RO=3;RPL=64;RPP=3.0274;RPPR=3.73412;RPR=63;RUN=1;SAF=76;SAP=13.6967;SAR=51;SRF=2;SRP=3.73412;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:130:3:103:127:4493:-395.11,-23.967,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
90 NC_000962 54394 . A G 3099.78 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=101;CIGAR=1X;DP=103;DPB=103;DPRA=0;EPP=3.0318;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=69.4356;MQMR=70;NS=1;NUMALT=1;ODDS=119.471;PAIRED=0.990099;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=3536;QR=62;RO=2;RPL=51;RPP=3.0318;RPPR=3.0103;RPR=50;RUN=1;SAF=42;SAP=9.22372;SAR=59;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:103:2:62:101:3536:-312.7,-21.3957,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
91 NC_000962 55553 . CC CCGTC 1280.36 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=53;CIGAR=1M3I1M;DP=55;DPB=137;DPRA=0;EPP=12.2288;EPPR=7.35324;GTI=0;LEN=3;MEANALT=1;MQM=73.5849;MQMR=70;NS=1;NUMALT=1;ODDS=57.7167;PAIRED=1;PAIREDR=1;PAO=2.5;PQA=70.5;PQR=70.5;PRO=2.5;QA=1550;QR=58;RO=2;RPL=18;RPP=14.851;RPPR=7.35324;RPR=35;RUN=1;SAF=13;SAP=32.8783;SAR=40;SRF=2;SRP=7.35324;SRR=0;TYPE=ins;technology.ILLUMINA=1;ANN=CCGTC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:55:2:58:53:1550:-134.282,-7.87492,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
92 NC_000962 57319 . C T 1836.41 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=70;CIGAR=1X;DP=70;DPB=70;DPRA=0;EPP=4.12706;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=101.646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2076;QR=0;RO=0;RPL=30;RPP=6.1124;RPPR=0;RPR=40;RUN=1;SAF=36;SAP=3.13438;SAR=34;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 1/1:70:0:0:70:2076:-187.137,-21.0721,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
93 NC_000962 57393 . A T 1215.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=45;CIGAR=1X;DP=45;DPB=45;DPRA=0;EPP=3.05855;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=66.9884;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1417;QR=0;RO=0;RPL=27;RPP=6.91895;RPPR=0;RPR=18;RUN=1;SAF=35;SAP=33.1696;SAR=10;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 1/1:45:0:0:45:1417:-127.845,-13.5463,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
94 NC_000962 62049 . A G 1946.06 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=65;CIGAR=1X;DP=65;DPB=65;DPRA=0;EPP=5.71629;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=94.7143;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2196;QR=0;RO=0;RPL=35;RPP=3.84548;RPPR=0;RPR=30;RUN=1;SAF=32;SAP=3.04371;SAR=33;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 1/1:65:0:0:65:2196:-197.978,-19.5669,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
95 NC_000962 62657 . G A 4190.52 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=151;CIGAR=1X;DP=151;DPB=151;DPRA=0;EPP=15.1044;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=213.936;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4741;QR=0;RO=0;RPL=69;RPP=5.44062;RPPR=0;RPR=82;RUN=1;SAF=98;SAP=32.131;SAR=53;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 1/1:151:0:0:151:4741:-427.004,-45.4555,0
f58178c0f00d planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 3e5c71977e50ec920d4f45be809d2528e55bff76
sanbi-uwc
parents: 0
diff changeset
96 NC_000962 66285 . C G 2136.27 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=69;CIGAR=1X;DP=71;DPB=71;DPRA=0;EPP=5.55942;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=74.2002;PAIRED=0.985507;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=2471;QR=73;RO=2;RPL=37;RPP=3.79707;RPPR=3.0103;RPR=32;RUN=1;SAF=35;SAP=3.04177;SAR=34;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.ILLUMINA=1;ANN=G||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:71:2:73:69:2471:-215.813,-11.0428,0