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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
| author | public-health-bioinformatics |
|---|---|
| date | Tue, 19 Sep 2023 18:03:41 +0000 |
| parents | |
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{ "qc": { "pct_reads_mapped": 99.47, "num_reads_mapped": 1731409, "median_coverage": 84, "gene_coverage": [ { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0005", "gene": "gyrB" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0006", "gene": "gyrA" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0407", "gene": "fgd1" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0486", "gene": "mshA" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0667", "gene": "rpoB" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0668", "gene": "rpoC" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0678", "gene": "mmpR5" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0682", "gene": "rpsL" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv0701", "gene": "rplC" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv1173", "gene": "fbiC" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv1267c", "gene": "embR" }, { "fraction": 0.0, "cutoff": 0, "locus_tag": "Rv1305", "gene": "atpE" }, { "fraction": 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] }, { "chrom": "Chromosome", "genome_pos": 9304, "ref": "G", "alt": "A", "freq": 1.0, "feature_id": "CCP42728", "type": "missense_variant", "nucleotide_change": "c.2003G>A", "protein_change": "p.Gly668Asp", "alternate_consequences": [], "change": "p.Gly668Asp", "locus_tag": "Rv0006", "gene": "gyrA", "gene_associated_drugs": [ "levofloxacin", "ciprofloxacin", "ofloxacin", "moxifloxacin", "fluoroquinolones" ] }, { "chrom": "Chromosome", "genome_pos": 766789, "ref": "G", "alt": "A", "freq": 1.0, "feature_id": "CCP43411", "type": "synonymous_variant", "nucleotide_change": "c.3420G>A", "protein_change": "p.Glu1140Glu", "alternate_consequences": [], "change": "c.3420G>A", "locus_tag": "Rv0668", "gene": "rpoC", "gene_associated_drugs": [ "rifampicin" ] }, { "chrom": "Chromosome", "genome_pos": 781395, "ref": "T", "alt": "C", "freq": 1.0, "feature_id": "CCP43425", "type": "upstream_gene_variant", "nucleotide_change": "c.-165T>C", "protein_change": "", "alternate_consequences": [], "change": 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"bedaquiline" ] }, { "chrom": "Chromosome", "genome_pos": 1471659, "ref": "C", "alt": "T", "freq": 1.0, "feature_id": "EBG00000313325-1", "type": "upstream_gene_variant", "nucleotide_change": "n.-187C>T", "protein_change": "", "alternate_consequences": [], "change": "n.-187C>T", "locus_tag": "EBG00000313325", "gene": "rrs", "gene_associated_drugs": [ "aminoglycosides", "streptomycin", "amikacin", "capreomycin", "kanamycin" ] }, { "chrom": "Chromosome", "genome_pos": 1917972, "ref": "A", "alt": "G", "freq": 1.0, "feature_id": "CCP44459", "type": "synonymous_variant", "nucleotide_change": "c.33A>G", "protein_change": "p.Leu11Leu", "alternate_consequences": [], "change": "c.33A>G", "locus_tag": "Rv1694", "gene": "tlyA", "gene_associated_drugs": [ "capreomycin" ] }, { "chrom": "Chromosome", "genome_pos": 3073868, "ref": "T", "alt": "C", "freq": 1.0, "feature_id": "CCP45563", "type": "missense_variant", "nucleotide_change": "c.604A>G", "protein_change": "p.Thr202Ala", "alternate_consequences": [], "change": "p.Thr202Ala", "locus_tag": "Rv2764c", "gene": "thyA", "gene_associated_drugs": [ "para-aminosalicylic_acid" ] }, { "chrom": "Chromosome", "genome_pos": 4242643, "ref": "C", "alt": "T", "freq": 1.0, "feature_id": "CCP46623", "type": "upstream_gene_variant", "nucleotide_change": "c.-590C>T", "protein_change": "", "alternate_consequences": [ { "gene_name": "embC", "gene_id": "Rv3793", "feature_id": "CCP46622", "type": "synonymous_variant", "nucleotide_change": "c.2781C>T", "protein_change": "p.Arg927Arg" } ], "change": "c.-590C>T", "locus_tag": "Rv3794", "gene": "embA", "gene_associated_drugs": [ "ethambutol" ] }, { "chrom": "Chromosome", "genome_pos": 1305494, "ref": "C", "alt": "<DEL>", "freq": 1.0, "feature_id": "CCP43929", "type": "frameshift_variant&stop_lost&splice_region_variant", "nucleotide_change": "c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", "protein_change": "p.Ala855fs", "alternate_consequences": [], "change": "c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN", "locus_tag": "Rv1173", "gene": "fbiC", "gene_associated_drugs": [ "delamanid" ] } ], "drtype": "MDR-TB", "db_version": { "name": "tbdb", "commit": "7fc199d", "Merge": "bad550a 277d053", "Author": "Jody Phelan <jody.phelan@lshtm.ac.uk>", "Date": "Tue Jan 25 17:21:48 2022 +0000" }, "id": "tbprofiler", "tbprofiler_version": "4.1.1", "pipeline": [ { "Analysis": "Mapping", "Program": "bwa" }, { "Analysis": "Variant calling", "Program": "freebayes" } ], "timestamp": "22-10-2022 01:09:50" }