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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler commit 7dba70c70c9fe33353a0fd21803b11cfddc42c32
| author | iuc |
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| date | Tue, 21 Oct 2025 10:24:27 +0000 |
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{ "schema_version": "1.0.0", "id": "ERR2510682", "timestamp": "2025-08-14T09:13:09.391314", "pipeline": { "software_version": "6.6.4", "db_version": { "name": "tbdb", "repo": "git@github.com:jodyphelan/tbdb.git", "branch": "tbdb", "commit": "3ed1cb99", "status": "clean", "author": "Jody Phelan", "date": "Sun Feb 16 11:08:45 2025 +0100", "db-schema-version": "2.0.0", "tb-profiler-version": ">=6.6.0,<7.0.0" }, "software": [ { "process": "variant_calling", "software": "freebayes", "version": "1.3.6" }, { "process": "long_variant_calling", "software": "delly", "version": "1.3.3" }, { "process": "depth_calculation", "software": "samtools", "version": "1.22" } ] }, "notes": [], "lineage": [ { "fraction": 100.0, "lineage": "lineage2", "family": "East-Asian", "rd": "RD105", "support": [ { "id": "lineage2", "chrom": "Chromosome", "pos": 39158, "target_allele_count": 37, "other_allele_count": 0, "all_allele_count": 37, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 282892, "target_allele_count": 23, "other_allele_count": 0, "all_allele_count": 23, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 497491, "target_allele_count": 41, "other_allele_count": 0, "all_allele_count": 41, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 811753, "target_allele_count": 42, "other_allele_count": 0, "all_allele_count": 42, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 1102468, "target_allele_count": 68, "other_allele_count": 0, "all_allele_count": 68, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 1317655, "target_allele_count": 18, "other_allele_count": 0, "all_allele_count": 18, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 1577241, "target_allele_count": 33, "other_allele_count": 0, "all_allele_count": 33, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 1980652, "target_allele_count": 23, "other_allele_count": 0, "all_allele_count": 23, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 4254431, "target_allele_count": 31, "other_allele_count": 0, "all_allele_count": 31, "target_allele_percent": 100.0 }, { "id": "lineage2", "chrom": "Chromosome", "pos": 4308395, "target_allele_count": 43, "other_allele_count": 0, "all_allele_count": 43, "target_allele_percent": 100.0 } ] }, { "fraction": 100.0, "lineage": "lineage2.2", "family": "East-Asian (Beijing)", "rd": "RD105;RD207", "support": [ { "id": "lineage2.2", "chrom": "Chromosome", "pos": 195682, "target_allele_count": 47, "other_allele_count": 0, "all_allele_count": 47, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 363464, "target_allele_count": 59, "other_allele_count": 0, "all_allele_count": 59, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 465300, "target_allele_count": 14, "other_allele_count": 2, "all_allele_count": 16, "target_allele_percent": 87.5 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 892416, "target_allele_count": 45, "other_allele_count": 1, "all_allele_count": 46, "target_allele_percent": 97.82608695652173 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 1288698, "target_allele_count": 60, "other_allele_count": 0, "all_allele_count": 60, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 1695037, "target_allele_count": 64, "other_allele_count": 0, "all_allele_count": 64, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 1849051, "target_allele_count": 40, "other_allele_count": 0, "all_allele_count": 40, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 2112832, "target_allele_count": 21, "other_allele_count": 0, "all_allele_count": 21, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 2202500, "target_allele_count": 22, "other_allele_count": 0, "all_allele_count": 22, "target_allele_percent": 100.0 }, { "id": "lineage2.2", "chrom": "Chromosome", "pos": 2505085, "target_allele_count": 29, "other_allele_count": 0, "all_allele_count": 29, "target_allele_percent": 100.0 } ] }, { "fraction": 100.0, "lineage": "lineage2.2.1", "family": "East-Asian (Beijing)", "rd": "RD105;RD207;RD181", "support": [ { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 135329, "target_allele_count": 18, "other_allele_count": 0, "all_allele_count": 18, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 163705, "target_allele_count": 24, "other_allele_count": 0, "all_allele_count": 24, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 215977, "target_allele_count": 21, "other_allele_count": 0, "all_allele_count": 21, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 533547, "target_allele_count": 19, "other_allele_count": 0, "all_allele_count": 19, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 797736, "target_allele_count": 52, "other_allele_count": 0, "all_allele_count": 52, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 1906078, "target_allele_count": 6, "other_allele_count": 1, "all_allele_count": 7, "target_allele_percent": 85.71428571428571 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 2078246, "target_allele_count": 45, "other_allele_count": 0, "all_allele_count": 45, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 2825581, "target_allele_count": 20, "other_allele_count": 0, "all_allele_count": 20, "target_allele_percent": 100.0 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 3498198, "target_allele_count": 51, "other_allele_count": 1, "all_allele_count": 52, "target_allele_percent": 98.07692307692307 }, { "id": "lineage2.2.1", "chrom": "Chromosome", "pos": 4158493, "target_allele_count": 27, "other_allele_count": 0, "all_allele_count": 27, "target_allele_percent": 100.0 } ] } ], "main_lineage": "lineage2", "sub_lineage": "lineage2.2.1", "spoligotype": null, "drtype": "Pre-XDR-TB", "dr_variants": [ { "chrom": "Chromosome", "pos": 7572, "ref": "T", "alt": "C", "depth": 24, "freq": 0.2916666666666667, "sv": false, "filter": "pass", "forward_reads": 4, "reverse_reads": 3, "sv_len": null, "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "change": "p.Ser91Pro", "nucleotide_change": "c.271T>C", "protein_change": "p.Ser91Pro", "annotation": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ], "consequences": [ { "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "nucleotide_change": "c.271T>C", "protein_change": "p.Ser91Pro", "sequence_hgvs": "Chromosome:g.7572T>C", "annotation": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Ser91Pro", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ], "locus_tag": "Rv0006", "gene_associated_drugs": [ "levofloxacin", "moxifloxacin" ] }, { "chrom": "Chromosome", "pos": 7582, "ref": "A", "alt": "G", "depth": 24, "freq": 0.6666666666666666, "sv": false, "filter": "pass", "forward_reads": 7, "reverse_reads": 9, "sv_len": null, "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "change": "p.Asp94Gly", "nucleotide_change": "c.281A>G", "protein_change": "p.Asp94Gly", "annotation": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ], "consequences": [ { "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "nucleotide_change": "c.281A>G", "protein_change": "p.Asp94Gly", "sequence_hgvs": "Chromosome:g.7582A>G", "annotation": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "levofloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "drug_resistance", "drug": "moxifloxacin", "original_mutation": "p.Asp94Gly", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ], "locus_tag": "Rv0006", "gene_associated_drugs": [ "levofloxacin", "moxifloxacin" ] }, { "chrom": "Chromosome", "pos": 761155, "ref": "C", "alt": "T", "depth": 29, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 15, "reverse_reads": 14, "sv_len": null, "gene_id": "Rv0667", "gene_name": "rpoB", "feature_id": "Rv0667", "type": "missense_variant", "change": "p.Ser450Leu", "nucleotide_change": "c.1349C>T", "protein_change": "p.Ser450Leu", "annotation": [ { "type": "drug_resistance", "drug": "rifampicin", "original_mutation": "p.Ser450Leu", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0667", "gene_name": "rpoB", "feature_id": "Rv0667", "type": "missense_variant", "nucleotide_change": "c.1349C>T", "protein_change": "p.Ser450Leu", "sequence_hgvs": "Chromosome:g.761155C>T", "annotation": [ { "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" }, { "type": "drug_resistance", "drug": "rifampicin", "original_mutation": "p.Ser450Leu", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "rifampicin", "original_mutation": "p.Ser450Leu", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "locus_tag": "Rv0667", "gene_associated_drugs": [ "rifampicin" ] }, { "chrom": "Chromosome", "pos": 781822, "ref": "A", "alt": "G", "depth": 52, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 24, "reverse_reads": 28, "sv_len": null, "gene_id": "Rv0682", "gene_name": "rpsL", "feature_id": "Rv0682", "type": "missense_variant", "change": "p.Lys88Arg", "nucleotide_change": "c.263A>G", "protein_change": "p.Lys88Arg", "annotation": [ { "type": "drug_resistance", "drug": "streptomycin", "original_mutation": "p.Lys88Arg", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0682", "gene_name": "rpsL", "feature_id": "Rv0682", "type": "missense_variant", "nucleotide_change": "c.263A>G", "protein_change": "p.Lys88Arg", "sequence_hgvs": "Chromosome:g.781822A>G", "annotation": [ { "type": "drug_resistance", "drug": "streptomycin", "original_mutation": "p.Lys88Arg", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "streptomycin", "original_mutation": "p.Lys88Arg", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "locus_tag": "Rv0682", "gene_associated_drugs": [ "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1673425, "ref": "C", "alt": "T", "depth": 49, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 20, "reverse_reads": 29, "sv_len": null, "gene_id": "Rv1484", "gene_name": "inhA", "feature_id": "Rv1484", "type": "upstream_gene_variant", "change": "c.-777C>T", "nucleotide_change": "c.-777C>T", "protein_change": "", "annotation": [ { "type": "drug_resistance", "drug": "ethionamide", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T" }, { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ], "consequences": [ { "gene_id": "Rv1484", "gene_name": "inhA", "feature_id": "Rv1484", "type": "upstream_gene_variant", "nucleotide_change": "c.-777C>T", "protein_change": "", "sequence_hgvs": "Chromosome:g.1673425C>T", "annotation": [ { "type": "drug_resistance", "drug": "ethionamide", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T" }, { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "ethionamide", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T" }, { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "c.-777C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)" } ], "locus_tag": "Rv1484", "gene_associated_drugs": [ "ethionamide", "isoniazid" ] }, { "chrom": "Chromosome", "pos": 2155168, "ref": "C", "alt": "G", "depth": 23, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 12, "reverse_reads": 11, "sv_len": null, "gene_id": "Rv1908c", "gene_name": "katG", "feature_id": "Rv1908c", "type": "missense_variant", "change": "p.Ser315Thr", "nucleotide_change": "c.944G>C", "protein_change": "p.Ser315Thr", "annotation": [ { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Ser315Thr", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ], "consequences": [ { "gene_id": "Rv1908c", "gene_name": "katG", "feature_id": "Rv1908c", "type": "missense_variant", "nucleotide_change": "c.944G>C", "protein_change": "p.Ser315Thr", "sequence_hgvs": "Chromosome:g.2155168C>G", "annotation": [ { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Ser315Thr", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Ser315Thr", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "High-level resistance" } ], "locus_tag": "Rv1908c", "gene_associated_drugs": [ "isoniazid" ] }, { "chrom": "Chromosome", "pos": 2289252, "ref": "T", "alt": "C", "depth": 33, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 17, "reverse_reads": 16, "sv_len": null, "gene_id": "Rv2043c", "gene_name": "pncA", "feature_id": "Rv2043c", "type": "upstream_gene_variant", "change": "c.-11A>G", "nucleotide_change": "c.-11A>G", "protein_change": "", "annotation": [ { "type": "drug_resistance", "drug": "pyrazinamide", "original_mutation": "c.-11A>G", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv2043c", "gene_name": "pncA", "feature_id": "Rv2043c", "type": "upstream_gene_variant", "nucleotide_change": "c.-11A>G", "protein_change": "", "sequence_hgvs": "Chromosome:g.2289252T>C", "annotation": [ { "type": "drug_resistance", "drug": "pyrazinamide", "original_mutation": "c.-11A>G", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "pyrazinamide", "original_mutation": "c.-11A>G", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "locus_tag": "Rv2043c", "gene_associated_drugs": [ "pyrazinamide" ] }, { "chrom": "Chromosome", "pos": 2715344, "ref": "G", "alt": "A", "depth": 49, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 26, "reverse_reads": 23, "sv_len": null, "gene_id": "Rv2416c", "gene_name": "eis", "feature_id": "Rv2416c", "type": "upstream_gene_variant", "change": "c.-12C>T", "nucleotide_change": "c.-12C>T", "protein_change": "", "annotation": [ { "type": "drug_resistance", "drug": "kanamycin", "original_mutation": "c.-12C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "amikacin", "original_mutation": "c.-12C>T", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv2416c", "gene_name": "eis", "feature_id": "Rv2416c", "type": "upstream_gene_variant", "nucleotide_change": "c.-12C>T", "protein_change": "", "sequence_hgvs": "Chromosome:g.2715344G>A", "annotation": [ { "type": "drug_resistance", "drug": "kanamycin", "original_mutation": "c.-12C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "amikacin", "original_mutation": "c.-12C>T", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "kanamycin", "original_mutation": "c.-12C>T", "confidence": "Assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "locus_tag": "Rv2416c", "gene_associated_drugs": [ "amikacin", "kanamycin" ] }, { "chrom": "Chromosome", "pos": 4243221, "ref": "C", "alt": "T", "depth": 45, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 20, "reverse_reads": 25, "sv_len": null, "gene_id": "Rv3794", "gene_name": "embA", "feature_id": "Rv3794", "type": "upstream_gene_variant", "change": "c.-12C>T", "nucleotide_change": "c.-12C>T", "protein_change": "", "annotation": [ { "type": "drug_resistance", "drug": "ethambutol", "original_mutation": "c.-12C>T", "confidence": "Uncertain significance", "source": "tbdb", "comment": "Mutation from literature: doi: 10.1128/AAC.03285-14" }, { "type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-12C>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv3794", "gene_name": "embA", "feature_id": "Rv3794", "type": "upstream_gene_variant", "nucleotide_change": "c.-12C>T", "protein_change": "", "sequence_hgvs": "Chromosome:g.4243221C>T", "annotation": [ { "type": "drug_resistance", "drug": "ethambutol", "original_mutation": "c.-12C>T", "confidence": "Uncertain significance", "source": "tbdb", "comment": "Mutation from literature: doi: 10.1128/AAC.03285-14" }, { "type": "who_confidence", "drug": "ethambutol", "original_mutation": "c.-12C>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "ethambutol", "original_mutation": "c.-12C>T", "confidence": "Uncertain significance", "source": "tbdb", "comment": "Mutation from literature: doi: 10.1128/AAC.03285-14" } ], "locus_tag": "Rv3794", "gene_associated_drugs": [ "ethambutol" ] }, { "chrom": "Chromosome", "pos": 4247513, "ref": "T", "alt": "C", "depth": 45, "freq": 0.9111111111111111, "sv": false, "filter": 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"source": "tbdb", "comment": "Mutation from literature" }, { "type": "who_confidence", "drug": "ethambutol", "original_mutation": "p.Tyr334His", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "drugs": [ { "type": "drug_resistance", "drug": "ethambutol", "original_mutation": "p.Tyr334His", "confidence": "Uncertain significance", "source": "tbdb", "comment": "Mutation from literature" } ], "locus_tag": "Rv3795", "gene_associated_drugs": [ "ethambutol" ] } ], "other_variants": [ { "chrom": "Chromosome", "pos": 7362, "ref": "G", "alt": "C", "depth": 63, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 29, "reverse_reads": 34, "sv_len": null, "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "change": "p.Glu21Gln", "nucleotide_change": "c.61G>C", "protein_change": "p.Glu21Gln", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Glu21Gln", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Glu21Gln", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "nucleotide_change": "c.61G>C", "protein_change": "p.Glu21Gln", "sequence_hgvs": "Chromosome:g.7362G>C", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Glu21Gln", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Glu21Gln", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0006", "gene_associated_drugs": [ "levofloxacin", "moxifloxacin" ] }, { "chrom": "Chromosome", "pos": 7585, "ref": "G", "alt": "C", "depth": 27, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 12, "reverse_reads": 15, "sv_len": null, "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "change": "p.Ser95Thr", "nucleotide_change": "c.284G>C", "protein_change": "p.Ser95Thr", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Ser95Thr", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Ser95Thr", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "nucleotide_change": "c.284G>C", "protein_change": "p.Ser95Thr", "sequence_hgvs": "Chromosome:g.7585G>C", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Ser95Thr", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Ser95Thr", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0006", "gene_associated_drugs": [ "levofloxacin", "moxifloxacin" ] }, { "chrom": "Chromosome", "pos": 9304, "ref": "G", "alt": "A", "depth": 38, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 18, "reverse_reads": 20, "sv_len": null, "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "change": "p.Gly668Asp", "nucleotide_change": "c.2003G>A", "protein_change": "p.Gly668Asp", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Gly668Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Gly668Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0006", "gene_name": "gyrA", "feature_id": "Rv0006", "type": "missense_variant", "nucleotide_change": "c.2003G>A", "protein_change": "p.Gly668Asp", "sequence_hgvs": "Chromosome:g.9304G>A", "annotation": [ { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "p.Gly668Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "p.Gly668Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0006", "gene_associated_drugs": [ "levofloxacin", "moxifloxacin" ] }, { "chrom": "Chromosome", "pos": 491742, "ref": "T", "alt": "C", "depth": 48, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 30, "reverse_reads": 18, "sv_len": null, "gene_id": "Rv0407", "gene_name": "fgd1", "feature_id": "Rv0407", "type": "synonymous_variant", "change": "c.960T>C", "nucleotide_change": "c.960T>C", "protein_change": "p.Phe320Phe", "annotation": [ { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "c.960T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "delamanid", "original_mutation": "c.960T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "pretomanid", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" } ], "consequences": [ { "gene_id": "Rv0407", "gene_name": "fgd1", "feature_id": "Rv0407", "type": "synonymous_variant", "nucleotide_change": "c.960T>C", "protein_change": "p.Phe320Phe", "sequence_hgvs": "Chromosome:g.491742T>C", "annotation": [ { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "c.960T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "delamanid", "original_mutation": "c.960T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0407", "gene_associated_drugs": [ "clofazimine", "delamanid", "pretomanid" ] }, { "chrom": "Chromosome", "pos": 575907, "ref": "C", "alt": "T", "depth": 42, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 22, "reverse_reads": 20, "sv_len": null, "gene_id": "Rv0486", "gene_name": "mshA", "feature_id": "Rv0486", "type": "missense_variant", "change": "p.Ala187Val", "nucleotide_change": "c.560C>T", "protein_change": "p.Ala187Val", "annotation": [ { "type": "who_confidence", "drug": "ethionamide", "original_mutation": "p.Ala187Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "p.Ala187Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0486", "gene_name": "mshA", "feature_id": "Rv0486", "type": "missense_variant", "nucleotide_change": "c.560C>T", "protein_change": "p.Ala187Val", "sequence_hgvs": "Chromosome:g.575907C>T", "annotation": [ { "type": "who_confidence", "drug": "ethionamide", "original_mutation": "p.Ala187Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "p.Ala187Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0486", "gene_associated_drugs": [ "ethionamide", "isoniazid" ] }, { "chrom": "Chromosome", "pos": 620625, "ref": "A", "alt": "G", "depth": 44, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 26, "reverse_reads": 18, "sv_len": null, "gene_id": "Rv0529", "gene_name": "ccsA", "feature_id": "Rv0529", "type": "missense_variant", "change": "p.Ile245Met", "nucleotide_change": "c.735A>G", "protein_change": "p.Ile245Met", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "p.Ile245Met", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "p.Ile245Met", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "p.Ile245Met", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0529", "gene_name": "ccsA", "feature_id": "Rv0529", "type": "missense_variant", "nucleotide_change": "c.735A>G", "protein_change": "p.Ile245Met", "sequence_hgvs": "Chromosome:g.620625A>G", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "p.Ile245Met", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "p.Ile245Met", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "p.Ile245Met", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0529", "gene_associated_drugs": [ "amikacin", "capreomycin", "kanamycin" ] }, { "chrom": "Chromosome", "pos": 657081, "ref": "C", "alt": "T", "depth": 50, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 28, "reverse_reads": 22, "sv_len": null, "gene_id": "Rv0565c", "gene_name": "Rv0565c", "feature_id": "Rv0565c", "type": "synonymous_variant", "change": "c.390G>A", "nucleotide_change": "c.390G>A", "protein_change": "p.Val130Val", "annotation": [ { "type": "who_confidence", "drug": "ethionamide", "original_mutation": "c.390G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0565c", "gene_name": "Rv0565c", "feature_id": "Rv0565c", "type": 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"gene_name": "Rv0565c", "feature_id": "Rv0565c", "type": "missense_variant", "nucleotide_change": "c.329G>A", "protein_change": "p.Arg110His", "sequence_hgvs": "Chromosome:g.657142C>T", "annotation": [ { "type": "who_confidence", "drug": "ethionamide", "original_mutation": "p.Arg110His", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0565c", "gene_associated_drugs": [ "ethionamide" ] }, { "chrom": "Chromosome", "pos": 737293, "ref": "CA", "alt": "AC", "depth": 96, "freq": 0.11458333333333333, "sv": false, "filter": "pass", "forward_reads": 7, "reverse_reads": 4, "sv_len": null, "gene_id": "Rv0643c", "gene_name": "mmaA3", "feature_id": "Rv0643c", "type": "missense_variant", "change": "p.Cys286Val", "nucleotide_change": "c.856_857delTGinsGT", "protein_change": "p.Cys286Val", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" } ], "consequences": [ { "gene_id": "Rv0643c", "gene_name": "mmaA3", "feature_id": "Rv0643c", "type": "missense_variant", "nucleotide_change": "c.856_857delTGinsGT", "protein_change": "p.Cys286Val", "sequence_hgvs": "Chromosome:g.737293CA>AC", "annotation": [] } ], "locus_tag": "Rv0643c", "gene_associated_drugs": [ "isoniazid" ] }, { "chrom": "Chromosome", "pos": 738040, "ref": "C", "alt": "T", "depth": 100, "freq": 0.21, "sv": false, "filter": "pass", "forward_reads": 8, "reverse_reads": 13, "sv_len": null, "gene_id": "Rv0643c", "gene_name": "mmaA3", "feature_id": "Rv0643c", "type": "missense_variant", "change": "p.Arg37Gln", "nucleotide_change": "c.110G>A", "protein_change": "p.Arg37Gln", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" } ], "consequences": [ { "gene_id": "Rv0643c", "gene_name": "mmaA3", "feature_id": "Rv0643c", "type": "missense_variant", "nucleotide_change": "c.110G>A", "protein_change": "p.Arg37Gln", "sequence_hgvs": "Chromosome:g.738040C>T", "annotation": [] } ], "locus_tag": "Rv0643c", "gene_associated_drugs": [ "isoniazid" ] }, { "chrom": "Chromosome", "pos": 763031, "ref": "T", "alt": "C", "depth": 28, "freq": 0.9642857142857143, "sv": false, "filter": "pass", "forward_reads": 14, "reverse_reads": 13, "sv_len": null, "gene_id": "Rv0667", "gene_name": "rpoB", "feature_id": "Rv0667", "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": "Rv0667", "type": "synonymous_variant", "nucleotide_change": "c.3225T>C", "protein_change": "p.Ala1075Ala", 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"original_mutation": "p.Glu1092Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0668", "gene_name": "rpoC", "feature_id": "Rv0668", "type": "missense_variant", "nucleotide_change": "c.3276A>C", "protein_change": "p.Glu1092Asp", "sequence_hgvs": "Chromosome:g.766645A>C", "annotation": [ { "type": "who_confidence", "drug": "rifampicin", "original_mutation": "p.Glu1092Asp", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0668", "gene_associated_drugs": [ "rifampicin" ] }, { "chrom": "Chromosome", "pos": 775639, "ref": "T", "alt": "C", "depth": 12, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 7, "reverse_reads": 5, "sv_len": null, "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "change": "p.Ile948Val", "nucleotide_change": "c.2842A>G", "protein_change": "p.Ile948Val", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Ile948Val", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Ile948Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "nucleotide_change": "c.2842A>G", "protein_change": "p.Ile948Val", "sequence_hgvs": "Chromosome:g.775639T>C", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Ile948Val", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Ile948Val", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0676c", "gene_associated_drugs": [ "bedaquiline", "clofazimine" ] }, { "chrom": "Chromosome", "pos": 776100, "ref": "G", "alt": "A", "depth": 37, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 15, "reverse_reads": 22, "sv_len": null, "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "change": "p.Thr794Ile", "nucleotide_change": "c.2381C>T", "protein_change": "p.Thr794Ile", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Thr794Ile", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Thr794Ile", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "nucleotide_change": "c.2381C>T", "protein_change": "p.Thr794Ile", "sequence_hgvs": "Chromosome:g.776100G>A", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Thr794Ile", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Thr794Ile", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0676c", "gene_associated_drugs": [ "bedaquiline", "clofazimine" ] }, { "chrom": "Chromosome", "pos": 776182, "ref": "C", "alt": "T", "depth": 44, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 20, "reverse_reads": 24, "sv_len": null, "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "change": "p.Asp767Asn", "nucleotide_change": "c.2299G>A", "protein_change": "p.Asp767Asn", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Asp767Asn", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Asp767Asn", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "missense_variant", "nucleotide_change": "c.2299G>A", "protein_change": "p.Asp767Asn", "sequence_hgvs": "Chromosome:g.776182C>T", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "original_mutation": "p.Asp767Asn", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "clofazimine", "original_mutation": "p.Asp767Asn", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0676c", "gene_associated_drugs": [ "bedaquiline", "clofazimine" ] }, { "chrom": "Chromosome", "pos": 777128, "ref": "T", "alt": "C", "depth": 68, "freq": 0.1323529411764706, "sv": false, "filter": "pass", "forward_reads": 5, "reverse_reads": 4, "sv_len": null, "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "synonymous_variant", "change": "c.1353A>G", "nucleotide_change": "c.1353A>G", "protein_change": "p.Glu451Glu", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" }, { "type": "who_confidence", "drug": "clofazimine", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" } ], "consequences": [ { "gene_id": "Rv0676c", "gene_name": "mmpL5", "feature_id": "Rv0676c", "type": "synonymous_variant", "nucleotide_change": "c.1353A>G", "protein_change": "p.Glu451Glu", "sequence_hgvs": "Chromosome:g.777128T>C", "annotation": [] } ], "locus_tag": "Rv0676c", "gene_associated_drugs": [ "bedaquiline", "clofazimine" ] }, { "chrom": "Chromosome", "pos": 779615, "ref": "G", "alt": "C", "depth": 53, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 24, "reverse_reads": 29, "sv_len": null, "gene_id": "Rv0677c", "gene_name": "mmpS5", "feature_id": "Rv0677c", "type": "upstream_gene_variant", "change": "c.-710C>G", "nucleotide_change": "c.-710C>G", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "bedaquiline", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" }, { "type": "who_confidence", "drug": "clofazimine", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" } ], "consequences": [ { "gene_id": "Rv0677c", "gene_name": "mmpS5", "feature_id": "Rv0677c", "type": "upstream_gene_variant", "nucleotide_change": "c.-710C>G", "protein_change": "", "sequence_hgvs": "Chromosome:g.779615G>C", "annotation": [] } ], "locus_tag": "Rv0677c", "gene_associated_drugs": [ "bedaquiline", "clofazimine" ] }, { "chrom": "Chromosome", "pos": 781395, "ref": "T", "alt": "C", "depth": 39, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 17, "reverse_reads": 22, "sv_len": null, "gene_id": "Rv0682", "gene_name": "rpsL", "feature_id": "Rv0682", "type": "upstream_gene_variant", "change": "c.-165T>C", "nucleotide_change": "c.-165T>C", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.-165T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv0682", "gene_name": "rpsL", "feature_id": "Rv0682", "type": "upstream_gene_variant", "nucleotide_change": "c.-165T>C", "protein_change": "", "sequence_hgvs": "Chromosome:g.781395T>C", "annotation": [ { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.-165T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv0682", "gene_associated_drugs": [ "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1254562, "ref": "A", "alt": "G", "depth": 94, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 39, "reverse_reads": 55, "sv_len": null, "gene_id": "Rv1129c", "gene_name": "Rv1129c", "feature_id": "Rv1129c", "type": "upstream_gene_variant", "change": "c.-28T>C", "nucleotide_change": "c.-28T>C", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "rifampicin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv1129c", "gene_name": "Rv1129c", "feature_id": "Rv1129c", "type": "upstream_gene_variant", "nucleotide_change": "c.-28T>C", "protein_change": "", "sequence_hgvs": "Chromosome:g.1254562A>G", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "levofloxacin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "moxifloxacin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "rifampicin", "original_mutation": "c.-28T>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv1129c", "gene_associated_drugs": [ "isoniazid", "levofloxacin", "moxifloxacin", "rifampicin" ] }, { "chrom": "Chromosome", "pos": 1364706, "ref": "G", "alt": "A", "depth": 38, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 17, "reverse_reads": 21, "sv_len": null, "gene_id": "Rv1221", "gene_name": "sigE", "feature_id": "Rv1221", "type": "synonymous_variant", "change": "c.294G>A", "nucleotide_change": "c.294G>A", "protein_change": "p.Leu98Leu", "annotation": [ { "type": "who_confidence", "drug": "pyrazinamide", "original_mutation": "c.294G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv1221", "gene_name": "sigE", "feature_id": "Rv1221", "type": "synonymous_variant", "nucleotide_change": "c.294G>A", "protein_change": "p.Leu98Leu", "sequence_hgvs": "Chromosome:g.1364706G>A", "annotation": [ { "type": "who_confidence", "drug": "pyrazinamide", "original_mutation": "c.294G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv1221", "gene_associated_drugs": [ "pyrazinamide" ] }, { "chrom": "Chromosome", "pos": 1406760, "ref": "T", "alt": "TG", "depth": 29, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 15, "reverse_reads": 14, "sv_len": null, "gene_id": "Rv1258c", "gene_name": "Rv1258c", "feature_id": "Rv1258c", "type": "frameshift_variant", "change": "c.580_581insC", "nucleotide_change": "c.580_581insC", "protein_change": "p.Glu194fs", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "pyrazinamide", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "Rv1258c", "gene_name": "Rv1258c", "feature_id": "Rv1258c", "type": "frameshift_variant", "nucleotide_change": "c.580_581insC", "protein_change": "p.Glu194fs", "sequence_hgvs": "Chromosome:g.1406760T>TG", "annotation": [ { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "isoniazid", "original_mutation": "p.Glu194fs", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "pyrazinamide", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "pyrazinamide", "original_mutation": "p.Glu194fs", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "LoF", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "p.Glu194fs", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "Rv1258c", "gene_associated_drugs": [ "isoniazid", "pyrazinamide", "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1471659, "ref": "C", "alt": "T", "depth": 76, "freq": 1.0, "sv": false, "filter": "pass", "forward_reads": 40, "reverse_reads": 36, "sv_len": null, "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "upstream_gene_variant", "change": "n.-187C>T", "nucleotide_change": "n.-187C>T", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "confidence": "Uncertain significance", "comment": "Not found in WHO catalogue", "source": "", "original_mutation": "" }, { "type": "who_confidence", "drug": "capreomycin", "confidence": "Uncertain significance", "comment": "Not found in WHO 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"gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "change": "n.699C>A", "nucleotide_change": "n.699C>A", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "nucleotide_change": "n.699C>A", "protein_change": "", "sequence_hgvs": "Chromosome:g.1472544C>A", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "n.699C>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "EBG00000313325", "gene_associated_drugs": [ "amikacin", "capreomycin", "kanamycin", "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1472545, "ref": "A", "alt": "T", "depth": 49, "freq": 0.22448979591836735, "sv": false, "filter": "pass", "forward_reads": 6, "reverse_reads": 5, "sv_len": null, "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "change": "n.700A>T", "nucleotide_change": "n.700A>T", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ], "consequences": [ { "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "nucleotide_change": "n.700A>T", "protein_change": "", "sequence_hgvs": "Chromosome:g.1472545A>T", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "n.700A>T", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "EBG00000313325", "gene_associated_drugs": [ "amikacin", "capreomycin", "kanamycin", "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1472566, "ref": "G", "alt": "A", "depth": 42, "freq": 0.19047619047619047, "sv": false, "filter": "pass", "forward_reads": 4, "reverse_reads": 4, "sv_len": null, "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "change": "n.721G>A", "nucleotide_change": "n.721G>A", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.721G>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.721G>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "kanamycin", "original_mutation": "n.721G>A", "confidence": "Uncertain 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"" }, { "type": "who_confidence", "drug": "streptomycin", "original_mutation": "n.721G>A", "confidence": "Uncertain significance", "source": "WHO catalogue v2", "comment": "" } ] } ], "locus_tag": "EBG00000313325", "gene_associated_drugs": [ "amikacin", "capreomycin", "kanamycin", "streptomycin" ] }, { "chrom": "Chromosome", "pos": 1472571, "ref": "G", "alt": "C", "depth": 41, "freq": 0.1951219512195122, "sv": false, "filter": "pass", "forward_reads": 4, "reverse_reads": 4, "sv_len": null, "gene_id": "EBG00000313325", "gene_name": "rrs", "feature_id": "EBG00000313325", "type": "non_coding_transcript_exon_variant", "change": "n.726G>C", "nucleotide_change": "n.726G>C", "protein_change": "", "annotation": [ { "type": "who_confidence", "drug": "amikacin", "original_mutation": "n.726G>C", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": "" }, { "type": "who_confidence", "drug": "capreomycin", "original_mutation": "n.726G>C", "confidence": "Uncertain significance", 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