Mercurial > repos > sanbi-uwc > vcf_to_alignment

annotate test-data/vcf3.vcf @ 2:a0c85f2d74a5 draft

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planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 9612f06b8c60520dc0a047ec072ced317c7796e4
author sanbi-uwc
date Wed, 01 Feb 2017 08:45:12 -0500
parents cc255feec53b
children f58178c0f00d
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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_15533.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">
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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">
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15 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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_15554.dat m_tuberculosis_H37Rv /cip0/software/galaxy/cbtgalaxydev/cbtgx/galaxy/database/datasets/015/dataset_15533.dat "
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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' ">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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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' ">
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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62 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT $i
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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63 gi|448814763|ref|NC_000962.3| 1977 . A G 3254.97 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=108;CIGAR=1X;DP=108;DPB=108;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=154.325;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3691;QR=0;RO=0;RPL=46;RPP=8.15749;RPPR=0;RPR=62;RUN=1;SAF=39;SAP=21.1059;SAR=69;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 1/1:108:0:0:108:3691:-332.532,-32.5112,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
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64 gi|448814763|ref|NC_000962.3| 4013 . T C 3338.1 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=104;CIGAR=1X;DP=104;DPB=104;DPRA=0;EPP=3.09382;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=148.78;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3748;QR=0;RO=0;RPL=60;RPP=8.35546;RPPR=0;RPR=44;RUN=1;SAF=51;SAP=3.09382;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 1/1:104:0:0:104:3748:-337.68,-31.3071,0
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diff changeset
65 gi|448814763|ref|NC_000962.3| 7362 . G C 3635.66 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=114;CIGAR=1X;DP=114;DPB=114;DPRA=0;EPP=3.31507;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=162.643;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4075;QR=0;RO=0;RPL=58;RPP=3.08649;RPPR=0;RPR=56;RUN=1;SAF=53;SAP=4.22937;SAR=61;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 1/1:114:0:0:114:4075:-367.107,-34.3174,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
66 gi|448814763|ref|NC_000962.3| 7585 . G C 2508.78 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=80;CIGAR=1X;DP=80;DPB=80;DPRA=0;EPP=4.74748;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=115.509;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2841;QR=0;RO=0;RPL=47;RPP=8.33041;RPPR=0;RPR=33;RUN=1;SAF=51;SAP=16.1477;SAR=29;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 1/1:80:0:0:80:2841:-256.045,-24.0824,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
67 gi|448814763|ref|NC_000962.3| 9138 . C G 3155.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=99;CIGAR=1X;DP=99;DPB=99;DPRA=0;EPP=14.6134;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=3553;QR=0;RO=0;RPL=47;RPP=3.55865;RPPR=0;RPR=52;RUN=1;SAF=52;SAP=3.55865;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 1/1:99:0:0:99:3553:-320.129,-29.802,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
68 gi|448814763|ref|NC_000962.3| 9304 . G A 2632.56 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=96;CIGAR=1X;DP=96;DPB=96;DPRA=0;EPP=3.37221;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=2973;QR=0;RO=0;RPL=53;RPP=5.27225;RPPR=0;RPR=43;RUN=1;SAF=37;SAP=13.9581;SAR=59;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 1/1:96:0:0:96:2973:-267.88,-28.8989,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
69 gi|448814763|ref|NC_000962.3| 11701 . G A 3645.85 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=130;CIGAR=1X;DP=132;DPB=132;DPRA=0;EPP=3.27756;EPPR=5.18177;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=170.56;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=4123;QR=37;RO=1;RPL=56;RPP=8.42228;RPPR=5.18177;RPR=74;RUN=1;SAF=69;SAP=4.07933;SAR=61;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 1/1:132:1:37:130:4123:-367.82,-33.8527,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
70 gi|448814763|ref|NC_000962.3| 11879 . A G 3090.32 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=97;CIGAR=1X;DP=97;DPB=97;DPRA=0;EPP=3.56996;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=139.076;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3492;QR=0;RO=0;RPL=64;RPP=24.5235;RPPR=0;RPR=33;RUN=1;SAF=45;SAP=4.10723;SAR=52;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 1/1:97:0:0:97:3492:-314.64,-29.1999,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
71 gi|448814763|ref|NC_000962.3| 14785 . T C 4202.39 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=131;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=16.9508;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=186.21;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4725;QR=0;RO=0;RPL=58;RPP=6.73993;RPPR=0;RPR=73;RUN=1;SAF=70;SAP=4.35297;SAR=61;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 1/1:131:0:0:131:4725:-425.611,-39.4349,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
72 gi|448814763|ref|NC_000962.3| 21795 . G A 775.59 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=30;CIGAR=1X;DP=30;DPB=30;DPRA=0;EPP=5.61607;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=46.194;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=900;QR=0;RO=0;RPL=20;RPP=10.2485;RPPR=0;RPR=10;RUN=1;SAF=12;SAP=5.61607;SAR=18;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 1/1:30:0:0:30:900:-81.3,-9.0309,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
73 gi|448814763|ref|NC_000962.3| 26959 . C G 3443.58 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=113;CIGAR=1X;DP=113;DPB=113;DPRA=0;EPP=23.9371;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=161.256;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3884;QR=0;RO=0;RPL=54;RPP=3.49071;RPPR=0;RPR=59;RUN=1;SAF=58;SAP=3.18325;SAR=55;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 1/1:113:0:0:113:3884:-349.904,-34.0164,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
74 gi|448814763|ref|NC_000962.3| 29641 . G A 2336.93 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=89;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=4.98658;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=127.985;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2638;QR=0;RO=0;RPL=42;RPP=3.62026;RPPR=0;RPR=47;RUN=1;SAF=37;SAP=8.49998;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 1/1:89:0:0:89:2638:-237.716,-26.7917,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
75 gi|448814763|ref|NC_000962.3| 33436 . C T 3004.85 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=111;CIGAR=1X;DP=111;DPB=111;DPRA=0;EPP=10.0725;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=158.484;PAIRED=0.990991;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3399;QR=0;RO=0;RPL=61;RPP=5.3774;RPPR=0;RPR=50;RUN=1;SAF=42;SAP=17.2716;SAR=69;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 1/1:111:0:0:111:3399:-306.216,-33.4143,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
76 gi|448814763|ref|NC_000962.3| 33464 . C T 2273.74 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=86;CIGAR=1X;DP=88;DPB=88;DPRA=0;EPP=11.1912;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=123.826;PAIRED=0.988372;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2602;QR=0;RO=0;RPL=57;RPP=22.806;RPPR=0;RPR=29;RUN=1;SAF=33;SAP=13.1102;SAR=53;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 1/1:88:0:0:86:2602:-234.388,-25.8886,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
77 gi|448814763|ref|NC_000962.3| 33841 . C G 4699.14 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=148;CIGAR=1X;DP=148;DPB=148;DPRA=0;EPP=14.5132;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=209.777;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5321;QR=0;RO=0;RPL=47;RPP=45.7942;RPPR=0;RPR=101;RUN=1;SAF=81;SAP=5.88603;SAR=67;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 1/1:148:0:0:148:5321:-479.25,-44.5524,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
78 gi|448814763|ref|NC_000962.3| 34044 . T C 4233.99 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=131;CIGAR=1X;DP=131;DPB=131;DPRA=0;EPP=5.81167;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=186.21;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4743;QR=0;RO=0;RPL=65;RPP=3.02688;RPPR=0;RPR=66;RUN=1;SAF=69;SAP=3.82253;SAR=62;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 1/1:131:0:0:131:4743:-427.232,-39.4349,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
79 gi|448814763|ref|NC_000962.3| 37031 . C G 2756.54 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=89;CIGAR=1X;DP=89;DPB=89;DPRA=0;EPP=26.4573;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=127.985;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3123;QR=0;RO=0;RPL=48;RPP=4.20583;RPPR=0;RPR=41;RUN=1;SAF=47;SAP=3.62026;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 1/1:89:0:0:89:3123:-281.421,-26.7917,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
80 gi|448814763|ref|NC_000962.3| 37553 . TTCATGACTCGGCTCGGCCCACT TTCATGACTCGGCTCGGCCCACTCATGACTCGGCTCGGCCCACT 552.847 . AB=0.45614;ABP=3.9627;AC=1;AF=0.5;AN=2;AO=26;CIGAR=1M21I22M;DP=57;DPB=104.826;DPRA=0;EPP=3.34437;EPPR=9.52472;GTI=0;LEN=21;MEANALT=5;MQM=70;MQMR=70;NS=1;NUMALT=1;ODDS=127.298;PAIRED=1;PAIREDR=0.962963;PAO=19.5;PQA=611.5;PQR=611.5;PRO=19.5;QA=710;QR=906;RO=27;RPL=15;RPP=4.34659;RPPR=61.6401;RPR=11;RUN=1;SAF=5;SAP=24.391;SAR=21;SRF=18;SRP=9.52472;SRR=9;TYPE=ins;technology.ILLUMINA=1;ANN=TTCATGACTCGGCTCGGCCCACTCATGACTCGGCTCGGCCCACT||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 0/1:57:27:906:26:710:-63.0404,0,-80.7353
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
81 gi|448814763|ref|NC_000962.3| 42967 . G C 2741.65 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=86;CIGAR=1X;DP=86;DPB=86;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=123.826;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3107;QR=0;RO=0;RPL=44;RPP=3.1113;RPPR=0;RPR=42;RUN=1;SAF=27;SAP=28.866;SAR=59;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 1/1:86:0:0:86:3107:-279.991,-25.8886,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
82 gi|448814763|ref|NC_000962.3| 55553 . CC CCGTC 974.998 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1M3I1M;DP=44;DPB=107.5;DPRA=0;EPP=8.43898;EPPR=3.0103;GTI=0;LEN=3;MEANALT=3;MQM=75.25;MQMR=70;NS=1;NUMALT=1;ODDS=38.4489;PAIRED=1;PAIREDR=1;PAO=3.5;PQA=103;PQR=103;PRO=3.5;QA=1201;QR=65;RO=2;RPL=10;RPP=24.725;RPPR=7.35324;RPR=30;RUN=1;SAF=15;SAP=8.43898;SAR=25;SRF=1;SRP=3.0103;SRR=1;TYPE=ins;technology.ILLUMINA=1;ANN=CCGTC||MODIFIER|||||||||||||ERROR_CHROMOSOME_NOT_FOUND GT:DP:RO:QR:AO:QA:GL 1/1:44:2:65:40:1201:-102.282,-3.78576,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
83 gi|448814763|ref|NC_000962.3| 62049 . A G 2283.26 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=73;CIGAR=1X;DP=73;DPB=73;DPRA=0;EPP=28.0269;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=105.805;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2599;QR=0;RO=0;RPL=39;RPP=3.75395;RPPR=0;RPR=34;RUN=1;SAF=32;SAP=5.41974;SAR=41;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 1/1:73:0:0:73:2599:-234.266,-21.9752,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
84 gi|448814763|ref|NC_000962.3| 63214 . C T 3898.32 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=140;CIGAR=1X;DP=140;DPB=140;DPRA=0;EPP=10.5174;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=198.686;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4379;QR=0;RO=0;RPL=63;RPP=6.05036;RPPR=0;RPR=77;RUN=1;SAF=68;SAP=3.25847;SAR=72;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 1/1:140:0:0:140:4379:-394.423,-42.1442,0
cc255feec53b planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit bc8fd85986b54f9d000e7d5869876fc9e479b6eb
sanbi-uwc
parents:
diff changeset
85 gi|448814763|ref|NC_000962.3| 67792 . C T 1827.25 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=69;CIGAR=1X;DP=69;DPB=69;DPRA=0;EPP=3.29354;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=70;MQMR=0;NS=1;NUMALT=1;ODDS=100.259;PAIRED=0.985507;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2078;QR=0;RO=0;RPL=40;RPP=6.81824;RPPR=0;RPR=29;RUN=1;SAF=44;SAP=14.3712;SAR=25;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 1/1:69:0:0:69:2078:-187.321,-20.7711,0