# HG changeset patch # User iuc # Date 1717186009 0 # Node ID 42818629ec4c6a95b05ac0c7d933bfc744c3c193 # Parent 4934c0ac61971118935e4aa1d25801dd8aedff5b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17 diff -r 4934c0ac6197 -r 42818629ec4c tbvcfreport.xml --- a/tbvcfreport.xml Thu Mar 17 07:33:00 2022 +0000 +++ b/tbvcfreport.xml Fri May 31 20:06:49 2024 +0000 @@ -1,8 +1,8 @@ - + - generate HTML report from SnpEff annotated M.tb VCF(s) - 0.1.10 + 1.0.0 tbvcfreport @@ -62,7 +62,7 @@ - +
@@ -102,7 +102,7 @@ 435V", "drug": "rifampicin"}], "other_variants": [{"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 763031, "type": "synonymous", "change": "c.3225T>C", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "3225T>C"}, {"sample": "rif_resistant", "chr": "Chromosome", "genome_pos": 1834177, "type": "synonymous", "change": "c.636A>C", "freq": 1.0, "locus_tag": "Rv1630", "gene": "rpsA", "_internal_change": "636A>C"}], "XDR": "", "MDR": "", "drtype": "Drug-resistant", "id": "rif_resistant", "tbprofiler_version": "2.1.0", "pipeline": {"mapper": "bwa", "variant_caller": "BCFtools"}} \ No newline at end of file +{ + "id": "tbprofiler", + "timestamp": "2024-05-31T15:43:38.437239", + "pipeline": { + "software_version": "6.2.1", + "db_version": { + "name": "tbdb", + "commit": "82777ea", + "Author": "Jody Phelan ", + "Date": "Sun Mar 17 01:14:00 2024 +0000" + }, + "software": [ + { + "process": "variant_calling", + "software": "freebayes" + }, + { + "process": "depth_calculation", + "software": "samtools" + } + ] + }, + "notes": [], + "lineage": [ + { + "fraction": 1.0, + "lineage": "lineage2.2.2", + "family": "East-Asian (Beijing)", + "rd": "RD105;RD207", + "support": [ + { + "id": "lineage2.2.2", + "chrom": "Chromosome", + "pos": 154990, + "target_allele_count": 47, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2.2.2", + "chrom": "Chromosome", + "pos": 346693, + "target_allele_count": 23, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2.2.2", + "chrom": "Chromosome", + "pos": 449194, + "target_allele_count": 22, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2.2.2", + "chrom": "Chromosome", + "pos": 1565566, + "target_allele_count": 46, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2.2.2", + "chrom": "Chromosome", + "pos": 2640807, + "target_allele_count": 49, + "other_allele_count": 0, + "target_allele_percent": 100.0 + } + ] + }, + { + "fraction": 0.9940119760479041, + "lineage": "lineage2", + "family": "East-Asian", + "rd": "RD105", + "support": [ + { + "id": "lineage2", + "chrom": "Chromosome", + "pos": 497491, + "target_allele_count": 64, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2", + "chrom": "Chromosome", + "pos": 811753, + "target_allele_count": 51, + "other_allele_count": 1, + "target_allele_percent": 98.07692307692307 + }, + { + "id": "lineage2", + "chrom": "Chromosome", + "pos": 4254431, + "target_allele_count": 51, + "other_allele_count": 0, + "target_allele_percent": 100.0 + } + ] + }, + { + "fraction": 1.0, + "lineage": "lineage2.2", + "family": "East-Asian (Beijing)", + "rd": "RD105;RD207", + "support": [ + { + "id": "lineage2.2", + "chrom": "Chromosome", + "pos": 1849051, + "target_allele_count": 77, + "other_allele_count": 0, + "target_allele_percent": 100.0 + }, + { + "id": "lineage2.2", + "chrom": "Chromosome", + "pos": 2505085, + "target_allele_count": 36, + "other_allele_count": 0, + "target_allele_percent": 100.0 + } + ] + } + ], + "main_lineage": "lineage2", + "sub_lineage": "lineage2.2.2", + "spoligotype": null, + "drtype": "RR-TB", + "dr_variants": [ + { + "chrom": "Chromosome", + "pos": 761110, + "ref": "A", + "alt": "T", + "depth": 43, + "freq": 1.0, + "sv": false, + "filter": "pass", + "forward_reads": 20, + "reverse_reads": 23, + "sv_len": null, + "gene_id": "Rv0667", + "gene_name": "rpoB", + "feature_id": "CCP43410", + "type": "missense_variant", + "change": "p.Asp435Val", + "nucleotide_change": "c.1304A>T", + "protein_change": "p.Asp435Val", + "annotation": [ + { + "type": "drug_resistance", + "drug": "rifampicin", + "original_mutation": "p.Asp435Val", + "confidence": "Assoc w R", + "source": "WHO catalogue v2", + "comment": "" + } + ], + "consequences": [ + { + "gene_id": "Rv0667", + "gene_name": "rpoB", + "feature_id": "CCP43410", + "type": "missense_variant", + "nucleotide_change": "c.1304A>T", + "protein_change": "p.Asp435Val", + "annotation": [ + { + "type": "drug_resistance", + "drug": "rifampicin", + "original_mutation": "p.Asp435Val", + "confidence": "Assoc w R", + "source": "WHO catalogue v2", + "comment": "" + }, + { + "type": "drug_resistance", + "drug": "rifampicin", + "original_mutation": "RRDR non-silent", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Expert rule: Non-silent variants in RRDR of rpoB" + } + ] + } + ], + "drugs": [ + { + "type": "drug_resistance", + "drug": "rifampicin", + "original_mutation": "p.Asp435Val", + "confidence": "Assoc w R", + "source": "WHO catalogue v2", + "comment": "" + } + ], + "locus_tag": "Rv0667", + "gene_associated_drugs": [ + "rifampicin" + ] + } + ], + "other_variants": [ + { + "chrom": "Chromosome", + "pos": 763031, + "ref": "T", + "alt": "C", + "depth": 66, + "freq": 1.0, + "sv": false, + "filter": "pass", + "forward_reads": 29, + "reverse_reads": 37, + "sv_len": null, + "gene_id": "Rv0667", + "gene_name": "rpoB", + "feature_id": "CCP43410", + "type": "synonymous_variant", + "change": "c.3225T>C", + "nucleotide_change": "c.3225T>C", + "protein_change": "p.Ala1075Ala", + "annotation": [ + { + "type": "who_confidence", + "drug": "rifampicin", + "original_mutation": "c.3225T>C", + "confidence": "Not assoc w R", + "source": "WHO catalogue v2", + "comment": "" + } + ], + "consequences": [ + { + "gene_id": "Rv0667", + "gene_name": "rpoB", + "feature_id": "CCP43410", + "type": "synonymous_variant", + "nucleotide_change": "c.3225T>C", + "protein_change": "p.Ala1075Ala", + "annotation": [ + { + "type": "who_confidence", + "drug": "rifampicin", + "original_mutation": "c.3225T>C", + "confidence": "Not assoc w R", + "source": "WHO catalogue v2", + "comment": "" + } + ] + }, + { + "gene_id": "Rv0668", + "gene_name": "rpoC", + "feature_id": "CCP43411", + "type": "upstream_gene_variant", + "nucleotide_change": "c.-339T>C", + "protein_change": "", + "annotation": [] + } + ], + "locus_tag": "Rv0667", + "gene_associated_drugs": [ + "rifampicin" + ] + }, + { + "chrom": "Chromosome", + "pos": 1834177, + "ref": "A", + "alt": "C", + "depth": 67, + "freq": 1.0, + "sv": false, + "filter": "pass", + "forward_reads": 40, + "reverse_reads": 27, + "sv_len": null, + "gene_id": "Rv1630", + "gene_name": "rpsA", + "feature_id": "CCP44394", + "type": "synonymous_variant", + "change": "c.636A>C", + "nucleotide_change": "c.636A>C", + "protein_change": "p.Arg212Arg", + "annotation": [ + { + "type": "who_confidence", + "drug": "pyrazinamide", + "original_mutation": "c.636A>C", + "confidence": "Not assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "" + } + ], + "consequences": [ + { + "gene_id": "Rv1630", + "gene_name": "rpsA", + "feature_id": "CCP44394", + "type": "synonymous_variant", + "nucleotide_change": "c.636A>C", + "protein_change": "p.Arg212Arg", + "annotation": [ + { + "type": "who_confidence", + "drug": "pyrazinamide", + "original_mutation": "c.636A>C", + "confidence": "Not assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "" + } + ] + } + ], + "locus_tag": "Rv1630", + "gene_associated_drugs": [ + "pyrazinamide" + ] + } + ], + "qc_fail_variants": [], + "qc": { + "percent_reads_mapped": 87.19, + "num_reads_mapped": 5507, + "target_median_depth": 0.0, + "genome_median_depth": 0.0, + "target_qc": [ + { + "target": "dnaA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "gyrB", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "gyrA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv0010c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fgd1", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "mshA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ccsA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv0565c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "hadA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "nusG", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rpoB", + "percent_depth_pass": 100.0, + "median_depth": 75.0 + }, + { + "target": "rpoC", + "percent_depth_pass": 6.61, + "median_depth": 0.0 + }, + { + "target": "mmpL5", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "mmpS5", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "mmpR5", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rpsL", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rplC", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv1129c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fbiC", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "sigE", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv1258c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "embR", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "atpE", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rrs", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rrl", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fabG1", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "inhA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rpsA", + "percent_depth_pass": 8.91, + "median_depth": 0.0 + }, + { + "target": "tsnR", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "tlyA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "bacA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ndh", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "katG", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "PPE35", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv1979c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "pncA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "kasA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "eis", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ahpC", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "folC", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv2477c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "pepQ", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ribD", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv2680", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv2681", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv2752c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "thyX", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "thyA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ald", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fbiD", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv3083", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "whiB7", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "Rv3236c", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "lpqB", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "mtrB", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "mtrA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fbiA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "fbiB", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "alr", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "rpoA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ddn", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "clpC1", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "panD", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "glpK", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "embC", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "embA", + "percent_depth_pass": 3.98, + "median_depth": 0.0 + }, + { + "target": "embB", + "percent_depth_pass": 3.89, + "median_depth": 0.0 + }, + { + "target": "aftB", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ubiA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ethA", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "ethR", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "whiB6", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + }, + { + "target": "gid", + "percent_depth_pass": 0.0, + "median_depth": 0.0 + } + ], + "missing_positions": [ + ] + }, + "linked_samples": [] +} diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant.vcf --- a/test-data/rif_resistant.vcf Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant.vcf Fri May 31 20:06:49 2024 +0000 @@ -1,53 +1,51 @@ ##fileformat=VCFv4.2 ##FILTER= -##bcftoolsVersion=1.9+htslib-1.9 -##bcftoolsCommand=mpileup --fasta-ref /home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa rif_resistant.bam -##reference=file:///home/pvh/Data/fasta/Mycobacterium_tuberculosis_h37rv.GCA_000195955.2.29.dna.chromosome.Chromosome.fa -##contig= -##ALT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= +##fileDate=20240531 +##source=freeBayes v1.3.2-dirty +##reference=reference/ref.fa +##contig= +##phasing=none +##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" +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= ##FORMAT= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##bcftools_callVersion=1.9+htslib-1.9 -##bcftools_callCommand=call --ploidy 1 -c -v rif_resistant.mpileup; Date=Tue Apr 2 06:47:33 2019 -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant.bam -MT_H37RV_BRD_V5 15890 . G A 225.007 . DP=58;VDB=0.0163018;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,24;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 154990 . G T 225.007 . DP=57;VDB=0.997362;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,18,38;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 346693 . G T 225.007 . DP=27;VDB=0.365109;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,14,12;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 449194 . G A 225.007 . DP=29;VDB=0.387982;SGB=-0.692976;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,5,21;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 497491 . G A 225.007 . DP=78;VDB=0.57291;SGB=-0.693147;MQSB=0.99133;MQ0F=0;AF1=1;AC1=1;DP4=0,0,53,24;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 761110 . A T 225.007 . DP=59;VDB=0.35459;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,32;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 763031 . T C 225.007 . DP=85;VDB=0.401561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,46;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 811753 . C T 225.007 . DP=55;VDB=0.241716;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,27,24;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 1565566 . C T 225.007 . DP=52;VDB=0.650985;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,13,36;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 1833729 . TCCCC TCCCCCC 12.7055 . INDEL;IDV=1;IMF=1;DP=1;SGB=-0.379885;MQ0F=0;AF1=1;AC1=1;DP4=0,0,0,1;MQ=54;FQ=-999 GT:PL 1:50,3,0 -MT_H37RV_BRD_V5 1834177 . A C 225.007 . DP=76;VDB=0.880419;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,42,29;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 1849051 . C T 225.007 . DP=86;VDB=0.199205;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,38,45;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 2505085 . G A 225.007 . DP=48;VDB=0.280048;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,32,13;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 2543395 . T C 225.007 . DP=88;VDB=0.167176;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,37,46;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 2640807 . G A 225.007 . DP=55;VDB=0.218547;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,29,21;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 2775361 . C T 225.007 . DP=99;VDB=0.0864314;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,46,44;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 2789798 . G T 225.007 . DP=72;VDB=0.231858;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,35;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 3477942 . A G 225.007 . DP=100;VDB=0.912557;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,45,52;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 3587446 . G A 225.007 . DP=59;VDB=0.0078857;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,33,24;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 4254431 . G A 225.007 . DP=58;VDB=0.120561;SGB=-0.693147;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,25,33;MQ=60;FQ=-999 GT:PL 1:255,0 -MT_H37RV_BRD_V5 4254477 . T C 225.007 . DP=30;VDB=0.000342098;SGB=-0.693021;MQSB=1;MQ0F=0;AF1=1;AC1=1;DP4=0,0,10,17;MQ=60;FQ=-999 GT:PL 1:255,0 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##bcftools_viewVersion=1.13+htslib-1.13 +##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 +##bcftools_annotateVersion=1.13+htslib-1.13 +##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 +##SnpEffVersion="5.0e (build 2021-03-09 06:01), by Pablo Cingolani" +##SnpEffCmd="SnpEff -noStats -no-downstream -no-upstream -no-utr ref snps.filt.vcf " +##INFO= +##INFO= +##INFO= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rif_resistant_fastq_gz +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 +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 diff -r 4934c0ac6197 -r 42818629ec4c test-data/rif_resistant_drug_resistance_report.html --- a/test-data/rif_resistant_drug_resistance_report.html Thu Mar 17 07:33:00 2022 +0000 +++ b/test-data/rif_resistant_drug_resistance_report.html Fri May 31 20:06:49 2024 +0000 @@ -21,120 +21,167 @@ rif_resistant Report +
+ + + + + + + + + + + + + + + + + + + + + + + + +
Lineage Info
LineageLineage support fractionFamilyRD
lineage20.9940119760479041East-AsianRD105
lineage2.2.21.0East-Asian (Beijing)RD105;RD207
+

TBProfiler + rel="noreferrer noopener">TB-Profiler Drug Resistance Report

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +
+

TB-Profiler version 6.2.1 with + database tbdb:82777ea (Sun Mar 17 01:14:00 2024 +0000)

+
+
+
+
- Disclaimer: - Drug resistance predictions are for Research Purposes Only and are produced by - TBProfiler. -
DrugResistanceSupporting Mutations
IsoniazidS
RifampicinR rpoB - (1.0 p.Asp435Val) -
EthambutolS
PyrazinamideS
StreptomycinS
EthionamideS
FluoroquinolonesS
+ + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+ Disclaimer: + Drug resistance predictions are for Research Purposes Only and are produced by + TB-Profiler. +
AmikacinS
CapreomycinS
KanamycinS
Para-aminosalicylic acidS
LinezolidS
CycloserineS
DelaminidS
ClofazimineS
BedaquilineS
AminoglycosidesS
+ Drug + Resistance + Supporting Mutations + + + + Isoniazid + S + + + + Rifampicin + R + rpoB + (1.0 p.Asp435Val) + + + + Ethambutol + S + + + + Pyrazinamide + S + + + + Streptomycin + S + + + + Ethionamide + S + + + + Fluoroquinolones + S + + + + Amikacin + S + + + + Capreomycin + S + + + + Kanamycin + S + + + + Para-aminosalicylic acid + S + + + + Linezolid + S + + + + Cycloserine + S + + + + Delamanid + S + + + + Clofazimine + S + + + + Bedaquiline + S + + + + Aminoglycosides + S + + + + Levofloxacin + S + + + + Moxifloxacin + S + + + + Pretomanid + S + + + +