diff test-data/prediction_2019/data/ERR2704812_L5.json @ 6:8e7e5a660942 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/prediction_2019/data/ERR2704812_L5.json	Fri Sep 22 17:24:02 2023 +0000
@@ -0,0 +1,157 @@
+{
+    "ERR2704812_L5": {
+        "susceptibility": {
+            "Ofloxacin": {
+                "predict": "S"
+            },
+            "Moxifloxacin": {
+                "predict": "S"
+            },
+            "Isoniazid": {
+                "predict": "R",
+                "called_by": {
+                    "ahpC_G-48A-G2726145A": {
+                        "variant": null,
+                        "genotype": [
+                            1,
+                            1
+                        ],
+                        "genotype_likelihoods": [
+                            -43297.59603037145,
+                            -99999999,
+                            -315.05757839655627
+                        ],
+                        "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": 360,
+                                    "min_non_zero_depth": 352,
+                                    "kmer_count": 7229,
+                                    "klen": 21
+                                }
+                            },
+                            "expected_depths": [
+                                332.0
+                            ],
+                            "contamination_depths": [],
+                            "filter": [],
+                            "conf": 42983
+                        },
+                        "_cls": "Call.VariantCall"
+                    }
+                }
+            },
+            "Kanamycin": {
+                "predict": "S"
+            },
+            "Ethambutol": {
+                "predict": "S"
+            },
+            "Streptomycin": {
+                "predict": "S"
+            },
+            "Ciprofloxacin": {
+                "predict": "S"
+            },
+            "Pyrazinamide": {
+                "predict": "S"
+            },
+            "Rifampicin": {
+                "predict": "R",
+                "called_by": {
+                    "rpoB_D435V-GAC761109GTC": {
+                        "variant": null,
+                        "genotype": [
+                            1,
+                            1
+                        ],
+                        "genotype_likelihoods": [
+                            -40815.43149991495,
+                            -99999999,
+                            -318.2103823437153
+                        ],
+                        "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": 344,
+                                    "min_non_zero_depth": 328,
+                                    "kmer_count": 6544,
+                                    "klen": 20
+                                }
+                            },
+                            "expected_depths": [
+                                332.0
+                            ],
+                            "contamination_depths": [],
+                            "filter": [],
+                            "conf": 40497
+                        },
+                        "_cls": "Call.VariantCall"
+                    }
+                }
+            },
+            "Amikacin": {
+                "predict": "S"
+            },
+            "Capreomycin": {
+                "predict": "S"
+            }
+        },
+        "phylogenetics": {
+            "phylo_group": {
+                "Mycobacterium_tuberculosis_complex": {
+                    "percent_coverage": 98.467,
+                    "median_depth": 332.0
+                }
+            },
+            "sub_complex": {
+                "Unknown": {
+                    "percent_coverage": -1,
+                    "median_depth": -1
+                }
+            },
+            "species": {
+                "Mycobacterium_africanum": {
+                    "percent_coverage": 64.333,
+                    "median_depth": 326
+                }
+            },
+            "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": [
+            "ERR2704812_1.fastq",
+            "ERR2704812_2.fastq"
+        ],
+        "version": {
+            "mykrobe-predictor": "v0.10.0",
+            "mykrobe-atlas": "v0.10.0"
+        },
+        "genotype_model": "kmer_count"
+    }
+}