comparison test-data/prediction_2019/data/ERR125628_MBOV.json @ 6:8e7e5a660942 draft

planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2

6:8e7e5a660942

{
    "ERR125628_MBOV": {
        "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_H57D-GTG2289071GTC": {
                        "variant": null,
                        "genotype": [
                            1,
                            1
                        ],
                        "genotype_likelihoods": [
                            -5562.061052007205,
                            -99999999,
                            -89.506424216315
                        ],
                        "info": {
                            "coverage": {
                                "reference": {
                                    "percent_coverage": 5.0,
                                    "median_depth": 0,
                                    "min_non_zero_depth": 44,
                                    "kmer_count": 44,
                                    "klen": 21
                                },
                                "alternate": {
                                    "percent_coverage": 100.0,
                                    "median_depth": 46,
                                    "min_non_zero_depth": 44,
                                    "kmer_count": 837,
                                    "klen": 19
                                }
                            },
                            "expected_depths": [
                                56.0
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 5473
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "Rifampicin": {
                "predict": "S"
            },
            "Amikacin": {
                "predict": "S"
            },
            "Capreomycin": {
                "predict": "S"
            }
        },
        "phylogenetics": {
            "phylo_group": {
                "Mycobacterium_tuberculosis_complex": {
                    "percent_coverage": 99.425,
                    "median_depth": 56.0
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_bovis": {
                    "percent_coverage": 65.402,
                    "median_depth": 48.0
                }
            },
            "lineage": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            }
        },
        "kmer": 21,
        "probe_sets": [
            "tb-species-170421.fasta.gz",
            "tb-hunt-probe-set-jan-03-2019.fasta.gz"
        ],
        "files": [
            "ERR125628_1.fastq",
            "ERR125628_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}