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view test-data/rif_resistant.results.json @ 4:9793bc5d741b draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit a8fe4cf3a77ffb0334533cccb57b7af5f7f89e3b
| author | iuc |
|---|---|
| date | Fri, 07 Jun 2024 14:29:45 +0000 |
| parents | 42818629ec4c |
| children |
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{ "id": "tbprofiler", "timestamp": "2024-05-31T15:43:38.437239", "pipeline": { "software_version": "6.2.1", "db_version": { "name": "tbdb", "commit": "82777ea", "Author": "Jody Phelan <jody.phelan@lshtm.ac.uk>", "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": 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