Mercurial > repos > nml > mykrobe_parser
diff test-data/prediction_2020/data/ERR2704812_L5.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/prediction_2020/data/ERR2704812_L5.json Fri Sep 22 17:24:02 2023 +0000 @@ -0,0 +1,209 @@ +{ + "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" + } +}