Mercurial > repos > iuc > tb_profiler_collate
diff test-data/ERR2510682.results.json @ 0:5b218b5eedb6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler commit 7dba70c70c9fe33353a0fd21803b11cfddc42c32
| author | iuc |
|---|---|
| date | Tue, 21 Oct 2025 10:24:27 +0000 |
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| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ERR2510682.results.json Tue Oct 21 10:24:27 2025 +0000 @@ -0,0 +1,10292 @@ +{ + "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", + 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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": 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