Mercurial > repos > nml > mykrobe_parser
view test-data/prediction_2020/data/ERR3335753_L1.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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{ "ERR3335753_L1": { "susceptibility": { "Ofloxacin": { "predict": "S" }, "Moxifloxacin": { "predict": "S" }, "Isoniazid": { "predict": "S" }, "Kanamycin": { "predict": "S" }, "Ethambutol": { "predict": "S" }, "Streptomycin": { "predict": "S" }, "Ciprofloxacin": { "predict": "S" }, "Pyrazinamide": { "predict": "r", "called_by": { "pncA_T389TG-A2288853CA": { "variant": null, "genotype": [ 0, 1 ], "genotype_likelihoods": [ -1707.2912821258215, -685.0256738025864, -10049.785656880731 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 131, "min_non_zero_depth": 128, "kmer_count": 2768, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 43, "min_non_zero_depth": 41, "kmer_count": 779, "klen": 19 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 1022 }, "_cls": "Call.VariantCall" }, "pncA_G390GG-C2288852CC": { "variant": null, "genotype": [ 0, 1 ], "genotype_likelihoods": [ -1736.2599622230955, -680.8401734761619, -9873.233821297094 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 130, "min_non_zero_depth": 128, "kmer_count": 2719, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 43, "min_non_zero_depth": 41, "kmer_count": 779, "klen": 19 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 1055 }, "_cls": "Call.VariantCall" }, "pncA_G391GG-C2288851CC": { "variant": null, "genotype": [ 0, 1 ], "genotype_likelihoods": [ -1738.6635171276575, -680.5372646726655, -9858.860191248112 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 130, "min_non_zero_depth": 128, "kmer_count": 2715, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 43, "min_non_zero_depth": 41, "kmer_count": 779, "klen": 19 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 1058 }, "_cls": "Call.VariantCall" } } }, "Rifampicin": { "predict": "R", "called_by": { "rpoB_L430P-CTG761094CCG": { "variant": null, "genotype": [ 1, 1 ], "genotype_likelihoods": [ -14797.71027662235, -2370.6712704022216, -210.1929350878079 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 5, "min_non_zero_depth": 3, "kmer_count": 101, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 190, "min_non_zero_depth": 188, "kmer_count": 3622, "klen": 20 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 14588 }, "_cls": "Call.VariantCall" } } }, "Amikacin": { "predict": "S" }, "Capreomycin": { "predict": "S" } }, "phylogenetics": { "phylo_group": { "Mycobacterium_tuberculosis_complex": { "percent_coverage": 99.69, "median_depth": 236.0 } }, "sub_complex": { "Unknown": { "percent_coverage": -1, "median_depth": -1 } }, "species": { "Mycobacterium_tuberculosis": { "percent_coverage": 98.335, "median_depth": 220 } }, "lineage": { "lineage": [ "lineage1.1.2" ], "calls_summary": { "lineage1.1.2": { "good_nodes": 3, "tree_depth": 3, "genotypes": { "lineage1": 1, "lineage1.1": 1, "lineage1.1.2": 1 } } }, "calls": { "lineage1.1.2": { "lineage1": { "G615938A": { "variant": "ref-G615938A?var_name=G615938A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G615938A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -21093.01908042143, -3131.7111098608775, -36.41722114142065 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 7, "min_non_zero_depth": 7, "kmer_count": 140, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 266, "min_non_zero_depth": 253, "kmer_count": 5283, "klen": 21 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 21057 }, "_cls": "Call.VariantCall" } }, "lineage1.1": { "G4404247A": { "variant": "ref-G4404247A?var_name=G4404247A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G4404247A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -18797.627911556006, -2876.301552830875, -17.415442468427592 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 3, "min_non_zero_depth": 3, "kmer_count": 89, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 233, "min_non_zero_depth": 222, "kmer_count": 4676, "klen": 21 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 18780 }, "_cls": "Call.VariantCall" } }, "lineage1.1.2": { "G2622402A": { "variant": "ref-G2622402A?var_name=G2622402A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G2622402A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -20293.11207308055, -3214.134387325289, -14.413062967015499 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 3, "min_non_zero_depth": 2, "kmer_count": 55, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 247, "min_non_zero_depth": 241, "kmer_count": 5008, "klen": 21 } }, "expected_depths": [ 236.0 ], "contamination_depths": [], "filter": [], "conf": 20279 }, "_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": [ "ERR3335753_1.fastq", "ERR3335753_2.fastq" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }