Mercurial > repos > iuc > tbvcfreport

annotate test-data/vcf_with_no_protein.vcf @ 3:42818629ec4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents 4934c0ac6197
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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1 ##fileformat=VCFv4.2
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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2 ##fileDate=20220316
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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3 ##source=freeBayes v1.1.0-dirty
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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4 ##reference=reference/ref.fa
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5 ##contig=<ID=Chromosome,length=4411532>
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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6 ##phasing=none
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7 ##commandline="freebayes -p 1 -q 20 -m 60 --min-coverage 10 -V -f reference/ref.fa snps.bam --region Chromosome:0-1121280"
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8 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
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10 ##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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13 ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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14 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
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15 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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16 ##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
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17 ##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
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18 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
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19 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
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20 ##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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21 ##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
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22 ##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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23 ##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
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24 ##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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25 ##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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26 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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27 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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28 ##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">
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29 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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30 ##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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31 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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32 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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33 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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34 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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35 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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36 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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37 ##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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38 ##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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39 ##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
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40 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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41 ##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.">
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42 ##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
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43 ##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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44 ##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
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45 ##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
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46 ##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
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47 ##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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48 ##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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49 ##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
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50 ##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
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51 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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52 ##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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53 ##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">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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54 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
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55 ##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
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56 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
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57 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
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58 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
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59 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
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60 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
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61 ##filter=/usr/local/tools/_conda/envs/__snippy@3.2/bin/snippy-vcf_filter --minqual 10 --mincov 10 --minfrac 0.9 snps.raw.vcf
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62 ##SnpEffVersion="4.3 (build 2016-07-03 08:26), by Pablo Cingolani"
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63 ##SnpEffCmd="SnpEff -no-downstream -no-upstream -no-intergenic -no-utr -noStats ref snps.filt.vcf "
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64 ##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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65 ##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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66 ##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' ">
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
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67 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT snps
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
68 Chromosome 4198611 . CGGGGGT CGGGGT 6312.89 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1M1D5M;DP=194;DPB=182.429;DPRA=0;EPP=3.11156;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1453.6;PAIRED=0.989637;PAIREDR=0;PAO=19;PQA=553.5;PQR=355.5;PRO=13;QA=6821;QR=0;RO=0;RPL=100;RPP=3.56161;RPPR=0;RPR=93;RUN=1;SAF=96;SAP=3.02155;SAR=97;SRF=0;SRP=0;SRR=0;TYPE=del GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,193:0:0:193:6821:-631.289,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
69 Chromosome 4200220 . G A 7422.62 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=234;CIGAR=1X;DP=234;DPB=234;DPRA=0;EPP=6.72222;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1709.12;PAIRED=0.991453;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8248;QR=0;RO=0;RPL=108;RPP=6.01695;RPPR=0;RPR=126;RUN=1;SAF=123;SAP=4.34659;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3753c|Rv3753c|transcript|TRANSCRIPT_Rv3753c|protein_coding|1/1|c.2C>T|p.Thr1Met|2/501|2/501|1/166||WARNING_TRANSCRIPT_NO_START_CODON GT:DP:AD:RO:QR:AO:QA:GL 1:234:0,234:0:0:234:8248:-742.262,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
70 Chromosome 4202383 . C A 4389.44 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=137;CIGAR=1X;DP=137;DPB=137;DPRA=0;EPP=3.02615;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1010.7;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=4876;QR=0;RO=0;RPL=65;RPP=3.78696;RPPR=0;RPR=72;RUN=1;SAF=74;SAP=4.92817;SAR=63;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3756c|Rv3756c|transcript|TRANSCRIPT_Rv3756c|protein_coding|1/1|c.231G>T|p.Val77Val|231/720|231/720|77/239|| GT:DP:AD:RO:QR:AO:QA:GL 1:137:0,137:0:0:137:4876:-438.944,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
71 Chromosome 4205120 . G A 5602.51 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=177;CIGAR=1X;DP=178;DPB=178;DPRA=0;EPP=14.8;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1290.03;PAIRED=0.988701;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6248;QR=21;RO=1;RPL=80;RPP=6.55581;RPPR=5.18177;RPR=97;RUN=1;SAF=89;SAP=3.02257;SAR=88;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3759c|Rv3759c|transcript|TRANSCRIPT_Rv3759c|protein_coding|1/1|c.254C>T|p.Pro85Leu|254/948|254/948|85/315|| GT:DP:AD:RO:QR:AO:QA:GL 1:178:1,177:1:21:177:6248:-560.251,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
72 Chromosome 4210876 . C T 8084.63 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=256;CIGAR=1X;DP=256;DPB=256;DPRA=0;EPP=4.23175;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1861.55;PAIRED=0.996094;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8984;QR=0;RO=0;RPL=139;RPP=7.11574;RPPR=0;RPR=117;RUN=1;SAF=117;SAP=7.11574;SAR=139;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3764c|Rv3764c|transcript|TRANSCRIPT_Rv3764c|protein_coding|1/1|c.134G>A|p.Arg45His|134/1428|134/1428|45/475|| GT:DP:AD:RO:QR:AO:QA:GL 1:256:0,256:0:0:256:8984:-808.463,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
73 Chromosome 4214747 . C T 6141.11 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=194;CIGAR=1X;DP=194;DPB=194;DPRA=0;EPP=3.41325;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1414.04;PAIRED=0.994845;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6823;QR=0;RO=0;RPL=114;RPP=15.9496;RPPR=0;RPR=80;RUN=1;SAF=98;SAP=3.05507;SAR=96;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3769|Rv3769|transcript|TRANSCRIPT_Rv3769|protein_coding|1/1|c.133C>T|p.His45Tyr|133/273|133/273|45/90|| GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,194:0:0:194:6823:-614.111,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
74 Chromosome 4215484 . C G 7180.37 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=225;CIGAR=1X;DP=225;DPB=225;DPRA=0;EPP=3.4832;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1653.34;PAIRED=0.991111;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7979;QR=0;RO=0;RPL=111;RPP=3.09716;RPPR=0;RPR=114;RUN=1;SAF=102;SAP=7.26639;SAR=123;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3770c|Rv3770c|transcript|TRANSCRIPT_Rv3770c|protein_coding|1/1|c.292G>C|p.Ala98Pro|292/576|292/576|98/191|| GT:DP:AD:RO:QR:AO:QA:GL 1:225:0,225:0:0:225:7979:-718.037,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
75 Chromosome 4216255 . G C 6090.49 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1X;DP=193;DPB=193;DPRA=0;EPP=7.07197;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1402.39;PAIRED=0.974093;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6767;QR=0;RO=0;RPL=99;RPP=3.29158;RPPR=0;RPR=94;RUN=1;SAF=89;SAP=5.54181;SAR=104;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1:193:0,193:0:0:193:6767:-609.049,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
76 Chromosome 4217557 . G A 4628.62 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=147;CIGAR=1X;DP=147;DPB=147;DPRA=0;EPP=4.20683;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1065.78;PAIRED=0.993197;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5142;QR=0;RO=0;RPL=78;RPP=4.20683;RPPR=0;RPR=69;RUN=1;SAF=76;SAP=3.3796;SAR=71;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3772|Rv3772|transcript|TRANSCRIPT_Rv3772|protein_coding|1/1|c.424G>A|p.Ala142Thr|424/1062|424/1062|142/353|| GT:DP:AD:RO:QR:AO:QA:GL 1:147:0,147:0:0:147:5142:-462.862,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
77 Chromosome 4223172 . C T 3477.35 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=110;CIGAR=1X;DP=110;DPB=110;DPRA=0;EPP=18.487;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=800.69;PAIRED=0.981818;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=3862;QR=0;RO=0;RPL=41;RPP=18.487;RPPR=0;RPR=69;RUN=1;SAF=28;SAP=60.5741;SAR=82;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv3777|Rv3777|transcript|TRANSCRIPT_Rv3777|protein_coding|1/1|c.479C>T|p.Ala160Val|479/987|479/987|160/328|| GT:DP:AD:RO:QR:AO:QA:GL 1:110:0,110:0:0:110:3862:-347.735,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
78 Chromosome 4232327 . G A 7703.92 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=242;CIGAR=1X;DP=243;DPB=243;DPRA=0;EPP=5.91756;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1773.89;PAIRED=0.995868;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8565;QR=0;RO=0;RPL=135;RPP=10.0452;RPPR=0;RPR=107;RUN=1;SAF=113;SAP=5.30739;SAR=129;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3785|Rv3785|transcript|TRANSCRIPT_Rv3785|protein_coding|1/1|c.1008G>A|p.Arg336Arg|1008/1074|1008/1074|336/357|| GT:DP:AD:RO:QR:AO:QA:GL 1:243:0,242:0:0:242:8565:-770.392,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
79 Chromosome 4238963 . C T 6583.6 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=214;CIGAR=1X;DP=216;DPB=216;DPRA=0;EPP=7.92148;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1515.93;PAIRED=0.985981;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7378;QR=60;RO=2;RPL=101;RPP=4.47148;RPPR=7.35324;RPR=113;RUN=1;SAF=99;SAP=5.60795;SAR=115;SRF=0;SRP=7.35324;SRR=2;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv3792|Rv3792|transcript|TRANSCRIPT_Rv3792|protein_coding|1/1|c.1032C>T|p.His344His|1032/1932|1032/1932|344/643|| GT:DP:AD:RO:QR:AO:QA:GL 1:216:2,214:2:60:214:7378:-658.36,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
80 Chromosome 4239274 . C G 7506.51 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=238;CIGAR=1X;DP=238;DPB=238;DPRA=0;EPP=7.42624;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1728.44;PAIRED=0.995798;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=8341;QR=0;RO=0;RPL=124;RPP=3.92268;RPPR=0;RPR=114;RUN=1;SAF=116;SAP=3.33876;SAR=122;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3792|Rv3792|transcript|TRANSCRIPT_Rv3792|protein_coding|1/1|c.1343C>G|p.Pro448Arg|1343/1932|1343/1932|448/643|| GT:DP:AD:RO:QR:AO:QA:GL 1:238:0,238:0:0:238:8341:-750.651,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
81 Chromosome 4240671 . T C 6428.63 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=203;CIGAR=1X;DP=203;DPB=203;DPRA=0;EPP=5.4171;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1480.25;PAIRED=0.980296;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7143;QR=0;RO=0;RPL=89;RPP=9.69587;RPPR=0;RPR=114;RUN=1;SAF=92;SAP=6.87188;SAR=111;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3793|Rv3793|transcript|TRANSCRIPT_Rv3793|protein_coding|1/1|c.809T>C|p.Ile270Thr|809/3285|809/3285|270/1094|| GT:DP:AD:RO:QR:AO:QA:GL 1:203:0,203:0:0:203:7143:-642.863,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
82 Chromosome 4247429 . A G 6696.64 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=211;CIGAR=1X;DP=212;DPB=212;DPRA=0;EPP=5.32585;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1541.96;PAIRED=0.990521;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7445;QR=0;RO=0;RPL=118;RPP=9.44239;RPPR=0;RPR=93;RUN=1;SAF=99;SAP=4.74954;SAR=112;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3795|Rv3795|transcript|TRANSCRIPT_Rv3795|protein_coding|1/1|c.916A>G|p.Met306Val|916/3297|916/3297|306/1098|| GT:DP:AD:RO:QR:AO:QA:GL 1:212:0,211:0:0:211:7445:-669.664,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
83 Chromosome 4247646 . C A 6787.39 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=223;CIGAR=1X;DP=224;DPB=224;DPRA=0;EPP=9.09627;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1562.85;PAIRED=0.982063;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=7580;QR=35;RO=1;RPL=106;RPP=4.18854;RPPR=5.18177;RPR=117;RUN=1;SAF=120;SAP=5.82445;SAR=103;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3795|Rv3795|transcript|TRANSCRIPT_Rv3795|protein_coding|1/1|c.1133C>A|p.Ala378Glu|1133/3297|1133/3297|378/1098|| GT:DP:AD:RO:QR:AO:QA:GL 1:224:1,223:1:35:223:7580:-678.739,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
84 Chromosome 4251297 . C G 6197.38 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=193;CIGAR=1X;DP=194;DPB=194;DPRA=0;EPP=3.29158;EPPR=0;GTI=0;LEN=1;MEANALT=2;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1427;PAIRED=0.984456;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=6891;QR=0;RO=0;RPL=96;RPP=3.02155;RPPR=0;RPR=97;RUN=1;SAF=91;SAP=4.37169;SAR=102;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3797|Rv3797|transcript|TRANSCRIPT_Rv3797|protein_coding|1/1|c.213C>G|p.Gly71Gly|213/1782|213/1782|71/593|| GT:DP:AD:RO:QR:AO:QA:GL 1:194:0,193:0:0:193:6891:-619.738,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
85 Chromosome 4254290 . T G 2461.94 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=79;CIGAR=1X;DP=79;DPB=79;DPRA=0;EPP=12.9331;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=566.884;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=2733;QR=0;RO=0;RPL=0;RPP=174.557;RPPR=0;RPR=79;RUN=1;SAF=30;SAP=12.9331;SAR=49;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3798|Rv3798|transcript|TRANSCRIPT_Rv3798|protein_coding|1/1|c.1298T>G|p.Leu433Arg|1298/1335|1298/1335|433/444|| GT:DP:AD:RO:QR:AO:QA:GL 1:79:0,79:0:0:79:2733:-246.194,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
86 Chromosome 4254478 . G A 7180.38 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=227;CIGAR=1X;DP=227;DPB=227;DPRA=0;EPP=3.09639;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1653.34;PAIRED=0.986784;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=7979;QR=0;RO=0;RPL=103;RPP=7.22889;RPPR=0;RPR=124;RUN=1;SAF=135;SAP=20.6978;SAR=92;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=A|missense_variant|MODERATE|Rv3799c|Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1471C>T|p.His491Tyr|1471/1569|1471/1569|491/522|| GT:DP:AD:RO:QR:AO:QA:GL 1:227:0,227:0:0:227:7979:-718.038,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
87 Chromosome 4261499 . A G 5307.9 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=171;CIGAR=1X;DP=171;DPB=171;DPRA=0;EPP=7.59452;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=1222.19;PAIRED=0.982456;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=5897;QR=0;RO=0;RPL=88;RPP=3.32777;RPPR=0;RPR=83;RUN=1;SAF=83;SAP=3.32777;SAR=88;SRF=0;SRP=0;SRR=0;TYPE=snp;ANN=G|missense_variant|MODERATE|Rv3801c|Rv3801c|transcript|TRANSCRIPT_Rv3801c|protein_coding|1/1|c.1568T>C|p.Val523Ala|1568/1914|1568/1914|523/637|| GT:DP:AD:RO:QR:AO:QA:GL 1:171:0,171:0:0:171:5897:-530.79,0
4934c0ac6197 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit eb93304c3aef325f02a62675d53c69a2b73c0fef"
iuc
parents:
diff changeset
88 Chromosome 4263279 . G A 6207.29 PASS AB=0;ABP=0;AC=1;AF=1;AN=1;AO=196;CIGAR=1X;DP=198;DPB=198;DPRA=0;EPP=9.39177;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=1429.28;PAIRED=0.994898;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=6971;QR=70;RO=2;RPL=100;RPP=3.18756;RPPR=7.35324;RPR=96;RUN=1;SAF=102;SAP=3.71935;SAR=94;SRF=1;SRP=3.0103;SRR=1;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1:198:2,196:2:70:196:6971:-620.729,0