Mercurial > repos > iuc > hamronize_tool
view test-data/mykrobe/mykrobe.json @ 4:cbfa52c8f1ef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
| author | iuc |
|---|---|
| date | Tue, 05 Mar 2024 19:47:12 +0000 |
| parents | |
| children |
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{ "SRR6916544": { "susceptibility": { "Rifampicin": { "predict": "r", "called_by": { "rpoB_S450L-TCG761154TTG": { "variant": null, "genotype": [ 0, 1 ], "genotype_likelihoods": [ -3594.140082249598, -136.57739012799902, -2127.6812715680494 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 40, "min_non_zero_depth": 32, "kmer_count": 796, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 60, "min_non_zero_depth": 58, "kmer_count": 1150, "klen": 20 } }, "expected_depths": [ 124 ], "contamination_depths": [], "filter": [], "conf": 3458 }, "_cls": "Call.VariantCall" } } } }, "phylogenetics": { "phylo_group": { "Mycobacterium_tuberculosis_complex": { "percent_coverage": 99.681, "median_depth": 124 } }, "sub_complex": { "Unknown": { "percent_coverage": -1, "median_depth": -1 } }, "species": { "Mycobacterium_tuberculosis": { "percent_coverage": 98.804, "median_depth": 121 } }, "lineage": { "lineage": [ "lineage2.2.10", "lineage3" ], "calls_summary": { "lineage2.2.10": { "good_nodes": 3, "tree_depth": 3, "genotypes": { "lineage2": 0.5, "lineage2.2": 0.5, "lineage2.2.10": 0.5 } }, "lineage3": { "good_nodes": 1, "tree_depth": 1, "genotypes": { "lineage3": 0.5 } } }, "calls": { "lineage2.2.10": { "lineage2": { "G497491A": { "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A", "genotype": [ 0, 1 ], "genotype_likelihoods": [ -4852.294042193726, -68.00214340670391, -4045.7527933854217 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 76, "min_non_zero_depth": 70, "kmer_count": 1498, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 85, "min_non_zero_depth": 82, "kmer_count": 1695, "klen": 21 } }, "expected_depths": [ 124 ], "contamination_depths": [], "filter": [], "conf": 4784 }, "_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": [ 0, 1 ], "genotype_likelihoods": [ -3967.5854789566783, -20.859193826341652, -3054.5971617777313 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 58, "min_non_zero_depth": 56, "kmer_count": 1160, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 69, "min_non_zero_depth": 64, "kmer_count": 1383, "klen": 21 } }, "expected_depths": [ 124 ], "contamination_depths": [], "filter": [], "conf": 3947 }, "_cls": "Call.VariantCall" } }, "lineage2.2.10": { "G1364706A": { "variant": "ref-G1364706A?var_name=G1364706A&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=G1364706A", "genotype": [ 0, 1 ], "genotype_likelihoods": [ -2360.5217287767423, -145.4041778818164, -3052.427673185898 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 51, "min_non_zero_depth": 47, "kmer_count": 1017, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 42, "min_non_zero_depth": 42, "kmer_count": 848, "klen": 21 } }, "expected_depths": [ 124 ], "contamination_depths": [], "filter": [], "conf": 2215 }, "_cls": "Call.VariantCall" } } }, "lineage3": { "lineage3": { "C3273107A": { "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A", "genotype": [ 0, 1 ], "genotype_likelihoods": [ -3093.863597972382, -19.52878016336399, -3761.204834296007 ], "info": { "coverage": { "reference": { "percent_coverage": 100.0, "median_depth": 66, "min_non_zero_depth": 64, "kmer_count": 1323, "klen": 21 }, "alternate": { "percent_coverage": 100.0, "median_depth": 58, "min_non_zero_depth": 54, "kmer_count": 1160, "klen": 21 } }, "expected_depths": [ 124 ], "contamination_depths": [], "filter": [], "conf": 3074 }, "_cls": "Call.VariantCall" } } } } } }, "kmer": 21, "probe_sets": [ "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-species-170421.fasta.gz", "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-hunt-probe-set-jan-03-2019.fasta.gz", "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz" ], "files": [ "../SRR6916544_1.fastq.gz", "../SRR6916544_2.fastq.gz" ], "version": { "mykrobe-predictor": "v0.10.0", "mykrobe-atlas": "v0.10.0" }, "genotype_model": "kmer_count" } }