{"id":"W3025462655","doi":"10.1038/s41598-020-64680-3","title":"High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data","year":2020,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":29,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada; University of Alberta; University of Guelph","funders":"Ontario Ministry of Research and Innovation; Natural Sciences and Engineering Research Council of Canada; Ontario Ministry of Agriculture, Food and Rural Affairs; Agricultural Research Service; Genome Canada; Ontario Genomics; Ministry of Agriculture, Food and Rural Affairs; University of Guelph; Aarhus Universitet; Genome Alberta; U.S. Department of Agriculture","keywords":"Copy-number variation; Biology; Population; Confidence interval; Genotype; Genetics; Whole genome sequencing; Identification (biology); Genome; Computational biology; Gene; Medicine; Internal medicine","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0004788337,0.0001471147,0.0001791568,0.00002627311,0.0001541384,0.0002659238,0.0003592718,0.00009957611,0.0002046043],"category_scores_gemma":[0.0001456245,0.0001499386,0.00002601028,0.0001721825,0.0001995545,0.0000360489,0.0003721322,0.00009190728,0.00006784002],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001512859,"about_ca_system_score_gemma":0.0002180772,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000694924,"about_ca_topic_score_gemma":0.0002434277,"domain_scores_codex":[0.9980009,0.00005760602,0.0004201394,0.001065542,0.0002079945,0.0002477742],"domain_scores_gemma":[0.998477,0.00001093277,0.0001850679,0.001105924,0.00008396496,0.0001370536],"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":[0.00001515192,0.0000215875,0.01379609,0.00001493226,0.000021669,0.000101214,0.0004401634,0.00007586288,0.9829167,0.00005850892,0.002475639,0.00006245977],"study_design_scores_gemma":[0.001338919,0.000141653,0.09483811,0.00009342915,0.000113756,0.0005293025,0.001582394,0.0002966213,0.6931606,0.0095821,0.1968963,0.001426858],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9960204,0.0003329823,0.000881689,0.000346887,0.001530275,0.0001854407,0.0004139609,0.00001440362,0.0002739321],"genre_scores_gemma":[0.993061,0.00002397142,0.001335848,0.0001624485,0.0001712704,0.000009876509,0.003688459,0.00001497255,0.001532164],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2897561,"threshold_uncertainty_score":0.6114319,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03148006511797602,"score_gpt":0.2569435305180535,"score_spread":0.2254634654000774,"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."}}