Mercurial > repos > nml > mykrobe_parser
diff test-data/single_2019/single2019.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/single_2019/single2019.json Fri Sep 22 17:24:02 2023 +0000 @@ -0,0 +1,231 @@ +{ + "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" + } +}