Mercurial > repos > nml > mykrobe_parser
view test-data/prediction_2020/data/SRR1710097_L2.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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{ "SRR1710097_L2": { "susceptibility": { "Ofloxacin": { "predict": "S" }, "Moxifloxacin": { "predict": "S" }, "Isoniazid": { "predict": "S" }, "Kanamycin": { "predict": "S" }, "Ethambutol": { "predict": "S" }, "Streptomycin": { "predict": "S" }, "Ciprofloxacin": { "predict": "S" }, "Pyrazinamide": { "predict": "S" }, "Rifampicin": { "predict": "S" }, "Amikacin": { "predict": "S" }, "Capreomycin": { "predict": "S" } }, "phylogenetics": { "phylo_group": { "Mycobacterium_tuberculosis_complex": { "percent_coverage": 99.686, "median_depth": 420 } }, "sub_complex": { "Unknown": { "percent_coverage": -1, "median_depth": -1 } }, "species": { "Mycobacterium_tuberculosis": { "percent_coverage": 98.909, "median_depth": 403.0 } }, "lineage": { "lineage": [ "lineage2.2.4" ], "calls_summary": { "lineage2.2.4": { "good_nodes": 3, "tree_depth": 3, "genotypes": { "lineage2": 1, "lineage2.2": 1, "lineage2.2.4": 1 } } }, "calls": { "lineage2.2.4": { "lineage2": { "G497491A": { "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -53081.870411575976, -99999999, -401.73206510437967 ], "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": 438, "min_non_zero_depth": 424, "kmer_count": 8731, "klen": 21 } }, "expected_depths": [ 420 ], "contamination_depths": [], "filter": [], "conf": 52680 }, "_cls": "Call.VariantCall" } }, "lineage2.2": { "G2505085A": { "variant": "ref-G2505085A?var_name=G2505085A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G2505085A", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -49633.185227023845, -99999999, -453.6542893522951 ], "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": 418, "min_non_zero_depth": 262, "kmer_count": 7876, "klen": 21 } }, "expected_depths": [ 420 ], "contamination_depths": [], "filter": [], "conf": 49180 }, "_cls": "Call.VariantCall" } }, "lineage2.2.4": { "A782634G": { "variant": "ref-A782634G?var_name=A782634G&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=A782634G", "genotype": [ 1, 1 ], "genotype_likelihoods": [ -52377.030507181364, -99999999, -405.20219781199785 ], "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": 427, "min_non_zero_depth": 414, "kmer_count": 8558, "klen": 21 } }, "expected_depths": [ 420 ], "contamination_depths": [], "filter": [], "conf": 51972 }, "_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": [ "SRR1710097_1.fastq", "SRR1710097_2.fastq" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }