Mercurial > repos > nml > mykrobe_parser
view test-data/prediction_2019/data/ERR3335753_L1.json @ 6:8e7e5a660942 draft
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
| author | nml |
|---|---|
| date | Fri, 22 Sep 2023 17:24:02 +0000 |
| parents | |
| 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": { "East_Africa_Indian_ocean": { "percent_coverage": 100.0, "median_depth": 193 } } }, "kmer": 21, "probe_sets": [ "tb-species-170421.fasta.gz", "tb-hunt-probe-set-jan-03-2019.fasta.gz" ], "files": [ "ERR3335753_1.fastq", "ERR3335753_2.fastq" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }