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annotate test-data/rif_resistant.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 02d81b994ef5
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02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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1 ##fileformat=VCFv4.2
02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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2 ##FILTER=<ID=PASS,Description="All filters passed">
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42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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3 ##fileDate=20240531
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4 ##source=freeBayes v1.3.2-dirty
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5 ##reference=reference/ref.fa
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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6 ##contig=<ID=Chromosome,length=4411532>
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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7 ##phasing=none
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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8 ##commandline="freebayes -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam --region Chromosome:0-1495040"
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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10 ##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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11 ##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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12 ##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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13 ##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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14 ##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">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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15 ##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
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02d81b994ef5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f337505deb06b66961f77a64bfae244f88c6a865"
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16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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17 ##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">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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19 ##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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20 ##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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21 ##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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22 ##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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23 ##bcftools_viewVersion=1.13+htslib-1.13
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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24 ##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=100.0 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Fri May 31 19:43:23 2024
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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25 ##bcftools_annotateVersion=1.13+htslib-1.13
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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26 ##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Fri May 31 19:43:24 2024
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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27 ##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani"
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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28 ##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-utr ref snps.filt.vcf "
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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29 ##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' ">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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30 ##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'">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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31 ##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'">
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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32 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant_fastq_gz
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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33 Chromosome 15890 . G A 1500.92 . AB=0;AO=48;DP=48;QA=1704;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0014c|GENE_Rv0014c|transcript|TRANSCRIPT_Rv0014c|protein_coding|1/1|c.1581C>T|p.Ser527Ser|1581/1881|1581/1881|527/626|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:48:1704:-153.63,-14.4494,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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34 Chromosome 154990 . G T 1358.62 . AB=0;AO=45;DP=45;QA=1558;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0127|GENE_Rv0127|transcript|TRANSCRIPT_Rv0127|protein_coding|1/1|c.759G>T|p.Arg253Arg|759/1368|759/1368|253/455|| GT:DP:RO:QR:AO:QA:GL 1/1:45:0:0:45:1558:-140.494,-13.5464,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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35 Chromosome 346693 . G T 635.034 . AB=0;AO=20;DP=20;QA=729;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0284|GENE_Rv0284|transcript|TRANSCRIPT_Rv0284|protein_coding|1/1|c.1059G>T|p.Ser353Ser|1059/3993|1059/3993|353/1330|| GT:DP:RO:QR:AO:QA:GL 1/1:20:0:0:20:729:-65.9317,-6.0206,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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36 Chromosome 449194 . G A 651.409 . AB=0;AO=23;DP=23;QA=782;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0372c|GENE_Rv0372c|transcript|TRANSCRIPT_Rv0372c|protein_coding|1/1|c.192C>T|p.Gly64Gly|192/756|192/756|64/251|| GT:DP:RO:QR:AO:QA:GL 1/1:23:0:0:23:782:-70.6929,-6.92369,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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37 Chromosome 497491 . G A 1816.74 . AB=0;AO=56;DP=56;QA=2057;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv0411c|GENE_Rv0411c|transcript|TRANSCRIPT_Rv0411c|protein_coding|1/1|c.810C>T|p.Asp270Asp|810/987|810/987|270/328|| GT:DP:RO:QR:AO:QA:GL 1/1:56:0:0:56:2057:-185.366,-16.8577,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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38 Chromosome 761110 . A T 1500.1 . AB=0;AO=47;DP=48;QA=1701;QR=0;RO=0;TYPE=snp;ANN=T|missense_variant|MODERATE|Rv0667|GENE_Rv0667|transcript|TRANSCRIPT_Rv0667|protein_coding|1/1|c.1304A>T|p.Asp435Val|1304/3519|1304/3519|435/1172|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:47:1701:-153.05,-14.1484,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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39 Chromosome 811753 . C T 1585.34 . AB=0;AO=48;DP=48;QA=1796;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv0715|GENE_Rv0715|transcript|TRANSCRIPT_Rv0715|protein_coding|1/1|c.12C>T|p.His4His|12/318|12/318|4/105|| GT:DP:RO:QR:AO:QA:GL 1/1:48:0:0:48:1796:-161.892,-14.4494,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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40 Chromosome 1565566 . C T 1332.75 . AB=0;AO=43;DP=43;QA=1534;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1391|GENE_Rv1391|transcript|TRANSCRIPT_Rv1391|protein_coding|1/1|c.126C>T|p.Pro42Pro|126/1257|126/1257|42/418|| GT:DP:RO:QR:AO:QA:GL 1/1:43:0:0:43:1534:-138.344,-12.9443,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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41 Chromosome 1834177 . A C 1769.09 . AB=0;AO=54;DP=54;QA=2006;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv1630|GENE_Rv1630|transcript|TRANSCRIPT_Rv1630|protein_coding|1/1|c.636A>C|p.Arg212Arg|636/1446|636/1446|212/481|| GT:DP:RO:QR:AO:QA:GL 1/1:54:0:0:54:2006:-180.776,-16.2556,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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42 Chromosome 1849051 . C T 2143.76 . AB=0;AO=65;DP=65;QA=2415;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv1640c|GENE_Rv1640c|transcript|TRANSCRIPT_Rv1640c|protein_coding|1/1|c.2985G>A|p.Pro995Pro|2985/3519|2985/3519|995/1172|| GT:DP:RO:QR:AO:QA:GL 1/1:65:0:0:65:2415:-217.563,-19.567,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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43 Chromosome 2505085 . G A 1199.98 . AB=0;AO=39;DP=39;QA=1425;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2231c|GENE_Rv2231c|transcript|TRANSCRIPT_Rv2231c|protein_coding|1/1|c.615C>T|p.Ala205Ala|615/1095|615/1095|205/364|| GT:DP:RO:QR:AO:QA:GL 1/1:39:0:0:39:1425:-128.53,-11.7402,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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44 Chromosome 2543395 . T C 1871.23 . AB=0;AO=58;DP=58;QA=2110;QR=0;RO=0;TYPE=snp;ANN=C|synonymous_variant|LOW|Rv2268c|GENE_Rv2268c|transcript|TRANSCRIPT_Rv2268c|protein_coding|1/1|c.882A>G|p.Glu294Glu|882/1470|882/1470|294/489|| GT:DP:RO:QR:AO:QA:GL 1/1:58:0:0:58:2110:-190.142,-17.4597,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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45 Chromosome 2640807 . G A 1341.77 . AB=0;AO=43;DP=43;QA=1519;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv2357c|GENE_Rv2357c|transcript|TRANSCRIPT_Rv2357c|protein_coding|1/1|c.258C>T|p.Val86Val|258/1392|258/1392|86/463|| GT:DP:RO:QR:AO:QA:GL 1/1:43:0:0:43:1519:-136.983,-12.9443,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
iuc
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46 Chromosome 2775361 . C T 2221.3 . AB=0;AO=69;DP=69;QA=2506;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2472|GENE_Rv2472|transcript|TRANSCRIPT_Rv2472|protein_coding|1/1|c.90C>T|p.Arg30Arg|90/294|90/294|30/97|| GT:DP:RO:QR:AO:QA:GL 1/1:69:0:0:69:2506:-225.745,-20.7711,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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47 Chromosome 2789798 . G T 2050.68 . AB=0;AO=62;DP=62;QA=2312;QR=0;RO=0;TYPE=snp;ANN=T|synonymous_variant|LOW|Rv2483c|GENE_Rv2483c|transcript|TRANSCRIPT_Rv2483c|protein_coding|1/1|c.1225C>A|p.Arg409Arg|1225/1743|1225/1743|409/580|| GT:DP:RO:QR:AO:QA:GL 1/1:62:0:0:62:2312:-208.29,-18.6639,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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48 Chromosome 3477942 . A G 2414.91 . AB=0;AO=75;DP=75;QA=2721;QR=0;RO=0;TYPE=snp;ANN=G|synonymous_variant|LOW|Rv3109|GENE_Rv3109|transcript|TRANSCRIPT_Rv3109|protein_coding|1/1|c.294A>G|p.Thr98Thr|294/1080|294/1080|98/359|| GT:DP:RO:QR:AO:QA:GL 1/1:75:0:0:75:2721:-245.092,-22.5773,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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49 Chromosome 3587446 . G A 1562.41 . AB=0;AO=49;DP=49;QA=1766;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3210c|GENE_Rv3210c|transcript|TRANSCRIPT_Rv3210c|protein_coding|1/1|c.94C>T|p.Leu32Leu|94/696|94/696|32/231|| GT:DP:RO:QR:AO:QA:GL 1/1:49:0:0:49:1766:-159.195,-14.7505,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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50 Chromosome 4254431 . G A 1391.26 . AB=0;AO=46;DP=46;QA=1617;QR=0;RO=0;TYPE=snp;ANN=A|synonymous_variant|LOW|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1518C>T|p.Asp506Asp|1518/1569|1518/1569|506/522|| GT:DP:RO:QR:AO:QA:GL 1/1:46:0:0:46:1617:-145.801,-13.8474,0
42818629ec4c planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
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parents: 0
diff changeset
51 Chromosome 4254477 . T C 760.909 . AB=0;AO=26;DP=26;QA=933;QR=0;RO=0;TYPE=snp;ANN=C|missense_variant|MODERATE|Rv3799c|GENE_Rv3799c|transcript|TRANSCRIPT_Rv3799c|protein_coding|1/1|c.1472A>G|p.His491Arg|1472/1569|1472/1569|491/522|| GT:DP:RO:QR:AO:QA:GL 1/1:26:0:0:26:933:-84.2834,-7.82678,0