{"id":"W2943601499","doi":"10.3389/fmicb.2019.00955","title":"Accurate Phylogenetic Relationships Among Mycobacterium bovis Strains Circulating in France Based on Whole Genome Sequencing and Single Nucleotide Polymorphism Analysis","year":2019,"lang":"en","type":"article","venue":"Frontiers in Microbiology","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":64,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Ministère de l'Agriculture, des Pêcheries et de l'Alimentation","keywords":"Phylogenetic tree; Biology; Single-nucleotide polymorphism; Genetics; Mycobacterium bovis; Genome; Whole genome sequencing; Phylogenetic relationship; Polymorphism (computer science); Genotype; Phylogenetics; Gene; Mycobacterium tuberculosis; Tuberculosis; Medicine","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001126071,0.0002786801,0.0004976141,0.002211775,0.0002813002,0.0008137946,0.0002680434,0.0006000458,0.0004849006],"category_scores_gemma":[0.001685415,0.0001323272,0.000355319,0.001116237,0.0001979387,0.0002217291,0.0002607208,0.0002953207,0.000277983],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004606434,"about_ca_system_score_gemma":0.0003709486,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.009167452,"about_ca_topic_score_gemma":0.009845722,"domain_scores_codex":[0.9989684,0.0003494131,0.00005727703,0.0002643719,0.0002109011,0.0001496469],"domain_scores_gemma":[0.9992176,0.000233056,0.0001805636,0.00006717071,0.0002248966,0.00007660323],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0005879163,0.00009763084,0.7154212,0.0002026843,0.0002355264,0.0005874988,0.001284527,0.001987627,0.2005306,0.0004274781,0.0007826801,0.0778547],"study_design_scores_gemma":[0.00001025805,0.0002027236,0.9847047,0.00003374852,0.00007777999,0.0007514883,0.0003485555,0.003467487,0.005775903,0.0001547807,0.004455073,0.00001756262],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9912099,0.001870334,0.004615951,0.0001391565,0.00001358914,0.00002422274,0.001375281,0.00004289452,0.0007087606],"genre_scores_gemma":[0.9887266,0.0005173397,0.007559509,0.0001028923,0.00002274684,0.00001791024,0.002708356,0.00001045739,0.0003342085],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.009167452,"threshold_uncertainty_score":0.01822823,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01950839847223895,"score_gpt":0.2377209517568724,"score_spread":0.2182125532846334,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}