comparison test-data/prediction_2020/data/ERR234162_L3.json @ 6:8e7e5a660942 draft

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

6:8e7e5a660942

{
    "ERR234162_L3": {
        "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": 99.797,
                    "median_depth": 157.0
                }
            },
            "sub_complex": {
                "Unknown": {
                    "percent_coverage": -1,
                    "median_depth": -1
                }
            },
            "species": {
                "Mycobacterium_tuberculosis": {
                    "percent_coverage": 99.33,
                    "median_depth": 142.0
                }
            },
            "lineage": {
                "lineage": [
                    "lineage3.1.1"
                ],
                "calls_summary": {
                    "lineage3.1.1": {
                        "good_nodes": 2,
                        "tree_depth": 3,
                        "genotypes": {
                            "lineage3": 1,
                            "lineage3.1": 0,
                            "lineage3.1.1": 1
                        }
                    }
                },
                "calls": {
                    "lineage3.1.1": {
                        "lineage3": {
                            "C3273107A": {
                                "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A",
                                "genotype": [
                                    1,
                                    1
                                ],
                                "genotype_likelihoods": [
                                    -22459.780019127742,
                                    -99999999,
                                    -183.28823056990717
                                ],
                                "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": 196,
                                            "min_non_zero_depth": 190,
                                            "kmer_count": 3895,
                                            "klen": 21
                                        }
                                    },
                                    "expected_depths": [
                                        157.0
                                    ],
                                    "contamination_depths": [],
                                    "filter": [],
                                    "conf": 22276
                                },
                                "_cls": "Call.VariantCall"
                            }
                        },
                        "lineage3.1": null,
                        "lineage3.1.1": {
                            "G1084911A": {
                                "variant": "ref-G1084911A?var_name=G1084911A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G1084911A",
                                "genotype": [
                                    1,
                                    1
                                ],
                                "genotype_likelihoods": [
                                    -18914.2001312626,
                                    -99999999,
                                    -142.3141204554317
                                ],
                                "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": 149,
                                            "min_non_zero_depth": 145,
                                            "kmer_count": 3039,
                                            "klen": 21
                                        }
                                    },
                                    "expected_depths": [
                                        157.0
                                    ],
                                    "contamination_depths": [],
                                    "filter": [],
                                    "conf": 18772
                                },
                                "_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": [
            "ERR234162_1.fastq",
            "ERR234162_2.fastq"
        ],
        "version": {
            "mykrobe-predictor": "v0.10.0",
            "mykrobe-atlas": "v0.10.0"
        },
        "genotype_model": "kmer_count"
    }
}