{"id":"W3205504088","doi":"10.3389/fgene.2021.729867","title":"A Comprehensive Comparison of Haplotype-Based Single-Step Genomic Predictions in Livestock Populations With Different Genetic Diversity Levels: A Simulation Study","year":2021,"lang":"en","type":"article","venue":"Frontiers in Genetics","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"Conselho Nacional de Desenvolvimento Científico e Tecnológico; Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Purdue University","keywords":"Haplotype; Single-nucleotide polymorphism; Linkage disequilibrium; Heritability; Biology; Genetics; Tag SNP; Quantitative trait locus; SNP; Purebred; Population; Trait; Genetic association; SNP genotyping; Evolutionary biology; Allele; Crossbreed; Genotype; Gene; Computer science; Medicine","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"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":[0.00355782,0.0006053598,0.001000568,0.0007243562,0.0005180783,0.0008969679,0.001257248,0.001638207,0.001266881],"category_scores_gemma":[0.007410657,0.0004483868,0.001283853,0.0008207987,0.0007023022,0.001047927,0.0006656849,0.0009076521,0.0001341194],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001090657,"about_ca_system_score_gemma":0.0009833772,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02850503,"about_ca_topic_score_gemma":0.01382513,"domain_scores_codex":[0.9994133,0.0003364778,0.00002382682,0.0001070081,0.00004724649,0.00007213689],"domain_scores_gemma":[0.9914718,0.007134114,0.0003081854,0.0003865233,0.0004889255,0.0002104594],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00007168237,0.00004266115,0.00691443,0.00001807772,0.00005560174,0.00005576584,0.00002766326,0.9907351,0.0001793813,0.0005411088,0.0001208995,0.001237702],"study_design_scores_gemma":[0.00002873869,0.00004496703,0.00182225,0.000007689211,0.00002018247,0.00001684409,0.0000239524,0.9972511,0.0001358021,0.0005719872,0.00006647959,0.000009978916],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9791228,0.0002037897,0.01839256,0.0001901896,0.00001421334,0.00004422752,0.0005872679,0.0001136329,0.001331372],"genre_scores_gemma":[0.9903357,0.00008789531,0.008302529,0.00006303425,0.000007372239,0.00007179445,0.0007227826,0.00002355198,0.0003852977],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02850503,"threshold_uncertainty_score":0.05667824,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05272643738210395,"score_gpt":0.2782128052221954,"score_spread":0.2254863678400915,"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."}}