{"id":"W2024424382","doi":"10.1186/s12864-015-1387-6","title":"Limitations of variable number of tandem repeat typing identified through whole genome sequencing of Mycobacterium avium subsp. paratuberculosis on a national and herd level","year":2015,"lang":"en","type":"article","venue":"BMC Genomics","topic":"Mycobacterium research and diagnosis","field":"Medicine","cited_by":76,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Prince Edward Island; Ministère de l'Agriculture, des Pêcheries et de l'Alimentation; SaskTel (Canada); Université de Montréal; University of Guelph; University of Calgary","funders":"Biotechnology and Biological Sciences Research Council; Alberta Livestock and Meat Agency; Dairy Farmers of Canada","keywords":"Biology; Paratuberculosis; Typing; Variable number tandem repeat; Genetics; Herd; Genetic diversity; Tandem repeat; Genome; Whole genome sequencing; Molecular epidemiology; Phylogenetic tree; Population; Computational biology; Mycobacterium; Genotype; Gene; Ecology","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01520061,0.0005022094,0.0006427446,0.001890316,0.0007385837,0.001805773,0.002063858,0.0007216563,0.0005642282],"category_scores_gemma":[0.03698355,0.0002867611,0.0004051902,0.002312043,0.001023935,0.0005996567,0.0009355739,0.0006694848,0.000365327],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002075873,"about_ca_system_score_gemma":0.00296056,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.2187094,"about_ca_topic_score_gemma":0.2908225,"domain_scores_codex":[0.9876506,0.003821155,0.0008347037,0.001847551,0.005019002,0.0008270142],"domain_scores_gemma":[0.971348,0.01438214,0.002807394,0.00310843,0.0076019,0.000752177],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0004563443,0.00008066878,0.7912384,0.001339622,0.0006143677,0.0003289386,0.002786138,0.004790344,0.04516099,0.001275761,0.004215348,0.147713],"study_design_scores_gemma":[0.00001488206,0.0001537703,0.9552408,0.0006109405,0.0003275391,0.0007107515,0.001788466,0.01177134,0.0102619,0.002125331,0.0169589,0.00003532885],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9171831,0.00938249,0.04276156,0.003252057,0.0002401073,0.0003282404,0.008173176,0.0002977681,0.01838146],"genre_scores_gemma":[0.9701361,0.001745819,0.02344918,0.001212294,0.00005942653,0.0001831863,0.002207113,0.00004170955,0.0009650372],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2187094,"threshold_uncertainty_score":0.4348726,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.2331188033590014,"score_gpt":0.3358275176940166,"score_spread":0.1027087143350152,"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."}}