Mercurial > repos > nml > mykrobe_parser
view test-data/single_2020/single2020.json @ 7:12b397ad8687 draft default tip
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 97945a3ad655f1a0f99f577d0d423124460d900a
| author | nml |
|---|---|
| date | Tue, 24 Oct 2023 21:28:06 +0000 |
| parents | 8e7e5a660942 |
| children |
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{ "ERR2704812_L5": { "susceptibility": { "Ofloxacin": { "predict": "S" }, "Moxifloxacin": { "predict": "S" }, "Isoniazid": { "predict": "R", "called_by": { "ahpC_G-48A-G2726145A": { "variant": null, "genotype": [ 1, 1 ], "genotype_likelihoods": [ -43297.59603037145, -99999999, -315.05757839655627 ], "info": { "coverage": { "reference": { "percent_coverage": 0.0, "median_depth": 0, "min_non_zero_depth": 0, "kmer_count": 0, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 360, "min_non_zero_depth": 352, "kmer_count": 7229, "klen": 21 } }, "expected_depths": [ 332.0 ], "contamination_depths": [], "filter": [], "conf": 42983 }, "_cls": "Call.VariantCall" } } }, "Kanamycin": { "predict": "S" }, "Ethambutol": { "predict": "S" }, "Streptomycin": { "predict": "S" }, "Ciprofloxacin": { "predict": "S" }, "Pyrazinamide": { "predict": "S" }, "Rifampicin": { "predict": "R", "called_by": { "rpoB_D435V-GAC761109GTC": { "variant": null, "genotype": [ 1, 1 ], "genotype_likelihoods": [ -40815.43149991495, -99999999, -318.2103823437153 ], "info": { "coverage": { "reference": { "percent_coverage": 0.0, "median_depth": 0, "min_non_zero_depth": 0, "kmer_count": 0, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 344, "min_non_zero_depth": 328, "kmer_count": 6544, "klen": 20 } }, "expected_depths": [ 332.0 ], "contamination_depths": [], "filter": [], "conf": 40497 }, "_cls": "Call.VariantCall" } } }, "Amikacin": { "predict": "S" }, "Capreomycin": { "predict": "S" } }, "phylogenetics": { "phylo_group": { "Mycobacterium_tuberculosis_complex": { "percent_coverage": 98.467, "median_depth": 332.0 } }, "sub_complex": { "Unknown": { "percent_coverage": -1, "median_depth": -1 } }, "species": { "Mycobacterium_africanum": { "percent_coverage": 64.333, "median_depth": 326 } }, "lineage": { "lineage": [ "lineage5" ], "calls_summary": { "lineage5": { "good_nodes": 1, "tree_depth": 1, "genotypes": { "lineage5": 1 } } }, "calls": { "lineage5": { "lineage5": { "C1799921A": { "variant": "ref-C1799921A?var_name=C1799921A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C1799921A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -40869.16316992115, -99999999, -318.61512332363264 ], "info": { "coverage": { "reference": { "percent_coverage": 0.0, "median_depth": 0, "min_non_zero_depth": 0, "kmer_count": 0, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 331, "min_non_zero_depth": 327, "kmer_count": 6635, "klen": 21 } }, "expected_depths": [ 332.0 ], "contamination_depths": [], "filter": [], "conf": 40551 }, "_cls": "Call.VariantCall" } } } } } }, "kmer": 21, "probe_sets": [ "tb-species-170421.fasta.gz", "tb-hunt-probe-set-jan-03-2019.fasta.gz", "tb.lineage.20200930.probes.fa.gz" ], "files": [ "ERR2704812_1.fastq", "ERR2704812_2.fastq" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }