{"id":"W3135522965","doi":"10.1186/s12711-021-00622-5","title":"Imputation accuracy to whole-genome sequence in Nellore cattle","year":2021,"lang":"en","type":"article","venue":"Genetics Selection Evolution","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":58,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Coordenação de Aperfeiçoamento de Pessoal de Nível Superior; Fundação de Amparo à Pesquisa do Estado de São Paulo","keywords":"Imputation (statistics); Biology; Single-nucleotide polymorphism; SNP; Population; Genotype; Genetics; 1000 Genomes Project; Genome-wide association study; Minor allele frequency; Whole genome sequencing; Statistics; Computational biology; Genome; Missing data; Mathematics; Gene","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":[0.01610965,0.0004439614,0.0009936213,0.001140641,0.0005296534,0.001438615,0.001437732,0.0009049735,0.001692249],"category_scores_gemma":[0.02347815,0.000317688,0.001043537,0.00150102,0.0005026054,0.0006945868,0.0009146281,0.0008396447,0.0005020703],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005888141,"about_ca_system_score_gemma":0.0005072779,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004372282,"about_ca_topic_score_gemma":0.00613026,"domain_scores_codex":[0.994568,0.002803455,0.0003084168,0.001403441,0.0006461077,0.0002705496],"domain_scores_gemma":[0.9823179,0.01242749,0.001238494,0.002371345,0.001453124,0.0001916945],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.003017834,0.0002077687,0.6685201,0.0005306163,0.00419262,0.0005695571,0.001149551,0.1278822,0.0216439,0.001645883,0.003866851,0.1667732],"study_design_scores_gemma":[0.0001090833,0.0003780651,0.6370317,0.0002085082,0.000870932,0.0009077747,0.0003129187,0.3353555,0.01390976,0.004646417,0.00613875,0.000130559],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8678308,0.001747441,0.1238187,0.0002486809,0.00003783509,0.0000484818,0.003717392,0.0006419449,0.001908603],"genre_scores_gemma":[0.9380752,0.0003205655,0.05093469,0.0001627462,0.00001921061,0.00006476697,0.009061268,0.0001669348,0.001194544],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01610965,"threshold_uncertainty_score":0.08519697,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01510537840200162,"score_gpt":0.2676349809321111,"score_spread":0.2525296025301095,"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."}}