{"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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00004353351,0.0002314044,0.0003614672,0.0001496509,0.0001106221,0.00001437105,0.0002110506,0.0001512938,0.00000857635],"category_scores_gemma":[0.00002670502,0.0002437637,0.00006450438,0.0002613699,0.0001256695,0.00000359655,0.0002154939,0.0001519911,5.537551e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000070564,"about_ca_system_score_gemma":0.0001282192,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003855532,"about_ca_topic_score_gemma":0.0008542766,"domain_scores_codex":[0.9983672,0.000211394,0.0004608314,0.0004683934,0.0002345693,0.0002576445],"domain_scores_gemma":[0.9991103,0.00002812454,0.0001590997,0.0004594725,0.0001641892,0.00007877064],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00009850553,0.0009311762,0.5428473,0.00001964786,0.0000408028,0.000001733847,0.0005001789,0.4531663,0.001596264,0.00000538106,0.00004169185,0.0007510654],"study_design_scores_gemma":[0.002020461,0.001407834,0.960041,0.00003418732,0.00009036732,0.000001635105,0.001780536,0.03262536,0.00147331,0.0001562443,0.0001270536,0.0002420551],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7568483,0.001401876,0.2408847,0.00001245535,0.000252969,0.000514975,0.00004202286,0.000008181848,0.00003455174],"genre_scores_gemma":[0.8907064,0.000009337662,0.1090513,0.00002532225,0.00004608211,0.00002177694,0.00007743278,0.00002548981,0.00003689648],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.420541,"threshold_uncertainty_score":0.9940395,"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."}}