{
    "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": [
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                            1
                        ],
                        "genotype_likelihoods": [
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                            -99999999,
                            -89.506424216315
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                        "info": {
                            "coverage": {
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                                    "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": [
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                            "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": {
                "lineage": [
                    "lineageBovis"
                ],
                "calls_summary": {
                    "lineageBovis": {
                        "good_nodes": 1,
                        "tree_depth": 1,
                        "genotypes": {
                            "lineageBovis": 1
                        }
                    }
                },
                "calls": {
                    "lineageBovis": {
                        "lineageBovis": {
                            "C1492605T": {
                                "variant": "ref-C1492605T?var_name=C1492605T&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=C1492605T",
                                "genotype": [
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                                    1
                                ],
                                "genotype_likelihoods": [
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                                    -102.4977035173431
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                                "info": {
                                    "coverage": {
                                        "reference": {
                                            "percent_coverage": 60.0,
                                            "median_depth": 1,
                                            "min_non_zero_depth": 1,
                                            "kmer_count": 12,
                                            "klen": 21
                                        },
                                        "alternate": {
                                            "percent_coverage": 100.0,
                                            "median_depth": 82,
                                            "min_non_zero_depth": 75,
                                            "kmer_count": 1670,
                                            "klen": 21
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                                    },
                                    "expected_depths": [
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                                    "contamination_depths": [],
                                    "filter": [],
                                    "conf": 7669
                                },
                                "_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": [
            "ERR125628_1.fastq",
            "ERR125628_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}