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annotate test-data/results_1.json @ 3:19793eecc9f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
author iuc
date Fri, 16 Aug 2019 16:26:31 -0400
parents 8529c9fd63ad
children
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8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
parents:
diff changeset
1 {"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], ["Chromosome", 1834260], ["Chromosome", 1834261], ["Chromosome", 1834262], ["Chromosome", 1834263], ["Chromosome", 1834264], ["Chromosome", 1834265], ["Chromosome", 1834266], ["Chromosome", 1834267], ["Chromosome", 1834268], ["Chromosome", 1834269], ["Chromosome", 1834270], ["Chromosome", 1834271], ["Chromosome", 1834272], ["Chromosome", 1834273], ["Chromosome", 4245997], ["Chromosome", 4245998], ["Chromosome", 4245999], ["Chromosome", 4246000], ["Chromosome", 4246001], ["Chromosome", 4246002], ["Chromosome", 4246003], ["Chromosome", 4246004], ["Chromosome", 4246005], ["Chromosome", 4246006], ["Chromosome", 4246007], ["Chromosome", 4246008], ["Chromosome", 4246009], ["Chromosome", 4246010], ["Chromosome", 4246011], ["Chromosome", 4246012], ["Chromosome", 4246155], ["Chromosome", 4246156], ["Chromosome", 4246157], ["Chromosome", 4246158], ["Chromosome", 4246159], ["Chromosome", 4246160], ["Chromosome", 4246161], ["Chromosome", 4246162], ["Chromosome", 4246163], ["Chromosome", 4246164], ["Chromosome", 4246165], ["Chromosome", 4246166], ["Chromosome", 4246167], ["Chromosome", 4246168], ["Chromosome", 4246169], ["Chromosome", 4246170], ["Chromosome", 4246171], ["Chromosome", 4246172], ["Chromosome", 4246173], ["Chromosome", 4246174], ["Chromosome", 4246175], ["Chromosome", 4246176], ["Chromosome", 4246177], ["Chromosome", 4246178], ["Chromosome", 4246179], ["Chromosome", 4246180], ["Chromosome", 4246181], ["Chromosome", 4246182], ["Chromosome", 4246183], ["Chromosome", 4246184], ["Chromosome", 4248018], ["Chromosome", 4248019], ["Chromosome", 4248020], ["Chromosome", 4248021], ["Chromosome", 4248022], ["Chromosome", 4248023], ["Chromosome", 4248024], ["Chromosome", 4248025], ["Chromosome", 4248026], ["Chromosome", 4248027], ["Chromosome", 4248028], ["Chromosome", 4248029], ["Chromosome", 4248030], ["Chromosome", 4248031], ["Chromosome", 4248032], ["Chromosome", 4248033], ["Chromosome", 4248034], ["Chromosome", 4248035], ["Chromosome", 4248036], ["Chromosome", 4248037], ["Chromosome", 4248038], ["Chromosome", 4248039], ["Chromosome", 4248040], ["Chromosome", 4248041], ["Chromosome", 4248042], ["Chromosome", 4248043], ["Chromosome", 4248044], ["Chromosome", 4248045], ["Chromosome", 4248046], ["Chromosome", 4248047], ["Chromosome", 4248184], ["Chromosome", 4248185], ["Chromosome", 4248186], ["Chromosome", 4248187], ["Chromosome", 4248188], ["Chromosome", 4248189], ["Chromosome", 4248190], ["Chromosome", 4248191], ["Chromosome", 4248192], ["Chromosome", 4248193], ["Chromosome", 4248194], ["Chromosome", 4248195], ["Chromosome", 4248196], ["Chromosome", 4248197], ["Chromosome", 4248198], ["Chromosome", 4248199], ["Chromosome", 4248200], ["Chromosome", 4248201], ["Chromosome", 4248202], ["Chromosome", 4248203], ["Chromosome", 4248204], ["Chromosome", 4248205], ["Chromosome", 4248206], ["Chromosome", 4248207], ["Chromosome", 4248208], ["Chromosome", 4248209], ["Chromosome", 4248210], ["Chromosome", 4248211], ["Chromosome", 4248212], ["Chromosome", 4248213], ["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"}}