annotate test-data/results_1.json @ 6:f7f32674f751 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 693ca73048b8f27e54c0659ffbb3d04e2ce9873a"

{"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], ["Chromosome", 763409], ["Chromosome", 763410], ["Chromosome", 763411], ["Chromosome", 763412], ["Chromosome", 763413], ["Chromosome", 763414], ["Chromosome", 763415], ["Chromosome", 763416], ["Chromosome", 763417], ["Chromosome", 763418], ["Chromosome", 763419], ["Chromosome", 763420], ["Chromosome", 1834082], ["Chromosome", 1834083], ["Chromosome", 1834084], ["Chromosome", 1834085], ["Chromosome", 1834086], ["Chromosome", 1834087], ["Chromosome", 1834088], ["Chromosome", 1834089], ["Chromosome", 1834090], ["Chromosome", 1834091], ["Chromosome", 1834092], ["Chromosome", 1834093], ["Chromosome", 1834094], ["Chromosome", 1834095], ["Chromosome", 1834251], ["Chromosome", 1834252], ["Chromosome", 1834253], ["Chromosome", 1834254], ["Chromosome", 1834255], ["Chromosome", 1834256], ["Chromosome", 1834257], ["Chromosome", 1834258], ["Chromosome", 1834259], 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["Chromosome", 4248214], ["Chromosome", 4248215]], "qc": {"pct_reads_mapped": 87.21, "num_reads_mapped": 5515}, "missing_regions": {"Rv0005": 1.0, "Rv0006": 1.0, "Rv0667": 0.0, "Rv0668": 0.9804707060590886, "Rv0678": 1.0, "Rv0682": 1.0, "Rv0701": 1.0, "Rv1267c": 1.0, "rrs": 1.0, "rrl": 1.0, "Rv1483": 1.0, "Rv1484": 1.0, "Rv1630": 0.9029247044181705, "Rv1694": 1.0, "Rv1908c": 1.0, "Rv2043c": 1.0, "Rv2245": 1.0, "Rv2416c": 1.0, "Rv2428": 1.0, "Rv2447c": 1.0, "Rv2671": 1.0, "Rv2754c": 1.0, "Rv2764c": 1.0, "Rv2780": 1.0, "Rv3261": 1.0, "Rv3423c": 1.0, "Rv3601c": 1.0, "Rv3793": 1.0, "Rv3794": 0.9575037147102526, "Rv3795": 0.9584344660194175, "Rv3854c": 1.0, "Rv3855": 1.0, "Rv3919c": 1.0}, "lineage": [{"lin": "lineage2", "family": "East-Asian", "spoligotype": "Beijing", "rd": "RD105", "frac": 1.0}, {"lin": "lineage2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD207", "rd": "RD105;RD207", "frac": 1.0}, {"lin": "lineage2.2.2", "family": "East-Asian (Beijing)", "spoligotype": "Beijing-RD105/RD207", "rd": "RD105;RD207", "frac": 1.0}], "main_lin": "lineage2", "sublin": "lineage2.2.2", "dr_variants": [{"sample": "tbprofiler", "chr": "Chromosome", "genome_pos": 761110, "type": "missense", "change": "p.Asp435Val", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "435D>435V", "drug": "rifampicin"}], "other_variants": [{"sample": "tbprofiler", "chr": "Chromosome", "genome_pos": 763031, "type": "synonymous", "change": "c.3225T>C", "freq": 1.0, "locus_tag": "Rv0667", "gene": "rpoB", "_internal_change": "3225T>C"}, {"sample": "tbprofiler", "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": "tbprofiler", "tbprofiler_version": "2.1.1", "pipeline": {"mapper": "bwa", "variant_caller": "BCFtools"}}