{"id":"W4315778117","doi":"10.12938/bmfh.2022-017","title":"Phylogenomic analysis in <i>Latilactobacillus sakei</i> by using polymorphisms detected by next-generation sequencing","year":2023,"lang":"en","type":"article","venue":"Bioscience of Microbiota Food and Health","topic":"Identification and Quantification in Food","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; Mitani Foundation for Research and Development; Research Organization of Information and Systems","keywords":"Phylogenetic tree; Biology; Lactobacillus sakei; Genetics; Whole genome sequencing; Locus (genetics); Haplotype; Genome; Computational biology; Gene; Genotype; Bacteria; Lactic acid","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006287938,0.0001552869,0.0002317499,0.0003252799,0.0002463186,0.00006643751,0.000203775,0.0001349906,0.000009586266],"category_scores_gemma":[0.00003187045,0.00016318,0.00007338671,0.001244212,0.0001850837,0.00001620097,0.00006155774,0.00005834029,0.000004488918],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009321838,"about_ca_system_score_gemma":0.0002961837,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009383649,"about_ca_topic_score_gemma":0.0005880481,"domain_scores_codex":[0.9983782,0.00009041841,0.0005011816,0.0005569162,0.0001329678,0.0003402981],"domain_scores_gemma":[0.9991801,0.000007217193,0.0003063036,0.0003168595,0.00007837917,0.000111151],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.000005977854,0.00003031872,0.0005961275,0.00001869571,0.0000249423,9.695375e-8,0.0001155318,0.00004888441,0.9969173,0.00004288514,0.001446853,0.0007523537],"study_design_scores_gemma":[0.0003510291,0.0002129409,0.01010427,0.00001643,0.00002793033,0.000005074965,0.00009014511,0.004252898,0.9823845,0.000003018936,0.002317297,0.0002344382],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9956505,0.0021954,0.0009727381,0.0005247184,0.0001285132,0.0002223482,0.0002754918,0.00001771395,0.00001259952],"genre_scores_gemma":[0.9978553,0.0007667125,0.0003771609,0.0001839564,0.00003026084,0.000005729563,0.0005998582,0.00001292308,0.0001680636],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01453281,"threshold_uncertainty_score":0.6654289,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0720813932267545,"score_gpt":0.2887583064801851,"score_spread":0.2166769132534306,"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."}}