{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005625808,0.0001374662,0.0003967033,0.0001009673,0.00004072322,0.00001794947,0.00009499579,0.0001103826,0.0000788525],"category_scores_gemma":[0.0008988031,0.0001347539,0.00008414048,0.0002544506,0.0001028313,0.0001496238,0.00007741646,0.0001189728,0.00002607955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002437111,"about_ca_system_score_gemma":0.000861407,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003298857,"about_ca_topic_score_gemma":0.00005294988,"domain_scores_codex":[0.9985591,0.00007579602,0.0005149093,0.0002494791,0.0003720739,0.0002287081],"domain_scores_gemma":[0.9981732,0.0003738008,0.0002407573,0.0002813552,0.0007735292,0.0001573357],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0008676824,0.0005128274,0.1563035,0.0008817377,0.0004205639,0.000008028003,0.005683429,0.0006526343,0.8243931,0.007605946,0.002496825,0.0001736941],"study_design_scores_gemma":[0.009958299,0.001611163,0.7859666,0.001087782,0.0008437253,0.0002239544,0.007636418,0.00154492,0.1691698,0.01116188,0.009832364,0.0009631614],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.988173,0.0003147777,0.0007871183,0.0001022108,0.0001161887,0.0003208567,0.0002964015,0.000011546,0.009877887],"genre_scores_gemma":[0.9829066,0.0002128639,0.0158667,0.00008690625,0.0001023845,0.00002733901,0.000155696,0.00002391459,0.0006175764],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6552234,"threshold_uncertainty_score":0.5495105,"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."}}