report.json

{
    "my_sample_name": {
        "susceptibility": {
            "Ofloxacin": {
                "predict": "S"
            },
            "Moxifloxacin": {
                "predict": "S"
            },
            "Isoniazid": {
                "predict": "R",
                "called_by": {
                    "inhA_I21T-ATC1674262ACT": {
                        "variant": null,
                        "genotype": [
                            1,
                            1
                        ],
                        "genotype_likelihoods": [
                            -467.0296062525409,
                            -99999999,
                            -8.903844781805352
                        ],
                        "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": 4,
                                    "min_non_zero_depth": 3,
                                    "kmer_count": 72,
                                    "klen": 20
                                }
                            },
                            "expected_depths": [
                                4
                            ],
                            "contamination_depths": [],
                            "filter": [],
                            "conf": 458
                        },
                        "_cls": "Call.VariantCall"
                    }
                }
            },
            "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": 95.435,
                    "median_depth": 4
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_tuberculosis": {
                    "percent_coverage": 94.177,
                    "median_depth": 4.0
                }
            },
            "lineage": {
                "European_American": {
                    "percent_coverage": 65.833,
                    "median_depth": 3.5
                }
            }
        },
        "kmer": 21,
        "probe_sets": [
            "/home/fin/miniconda3/envs/amrtest/lib/python3.7/site-packages/mykrobe/data/panels/tb-species-170421.fasta.gz",
            "/home/fin/miniconda3/envs/amrtest/lib/python3.7/site-packages/mykrobe/data/panels/tb-hunt-probe-set-jan-03-2019.fasta.gz"
        ],
        "files": [
            "reads.fq.gz"
        ],
        "version": {
            "mykrobe-predictor": "v0.8.1",
            "mykrobe-atlas": "v0.8.1"
        },
        "genotype_model": "kmer_count"
    }
}