{"id":"W3003940285","doi":"10.3389/fgene.2019.01384","title":"Genomic Diversity Evaluation of Populus trichocarpa Germplasm for Rare Variant Genetic Association Studies","year":2020,"lang":"en","type":"article","venue":"Frontiers in Genetics","topic":"Genetic Mapping and Diversity in Plants and Animals","field":"Biochemistry, Genetics and Molecular Biology","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"Natural Resources Canada; University of British Columbia; Canadian Forest Service; Université Laval","funders":"Biological and Environmental Research; Natural Sciences and Engineering Research Council of Canada; Office of Science; Oak Ridge National Laboratory; Joint Genome Institute; Compute Canada; U.S. Department of Energy","keywords":"Biology; Genome-wide association study; Genetics; Heritability; Genetic variation; Missing heritability problem; Genome; Genetic diversity; Genetic association; Populus trichocarpa; Germplasm; Genomics; Genetic architecture; Evolutionary biology; Population; Quantitative trait locus; Gene; Single-nucleotide polymorphism; Genotype","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":[0.0004414003,0.0001368101,0.0002546999,0.00005999002,0.0001161164,0.00001130054,0.000212431,0.0001533952,0.000005785195],"category_scores_gemma":[0.0004476038,0.0001485114,0.00009884289,0.0001099288,0.00003340319,0.000002465155,0.0002277266,0.000054388,0.000001448571],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007719338,"about_ca_system_score_gemma":0.0000901801,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009388609,"about_ca_topic_score_gemma":0.0000095072,"domain_scores_codex":[0.9987911,0.0001086914,0.0002666945,0.0003186526,0.0002929373,0.0002219171],"domain_scores_gemma":[0.9992549,0.00002346728,0.0001943729,0.0001469069,0.0003091458,0.00007125127],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0003984248,0.0001200725,0.8236941,0.0002132532,0.0006649427,0.000005236942,0.002181905,0.02005053,0.03493635,0.00001525452,0.1022539,0.01546604],"study_design_scores_gemma":[0.01758269,0.00325277,0.7680033,0.0001198617,0.002399683,0.00001388599,0.009813568,0.08268157,0.0429843,0.003562565,0.06765525,0.001930509],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9825841,0.007611713,0.008135806,0.0002615924,0.0005937623,0.0004904133,0.0001672638,0.000006705215,0.000148628],"genre_scores_gemma":[0.9825514,0.001792079,0.01498956,0.0002807945,0.0001874771,0.00001367391,0.00006239997,0.00001103491,0.0001115715],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06263105,"threshold_uncertainty_score":0.605612,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04855855256399511,"score_gpt":0.2699776608008668,"score_spread":0.2214191082368717,"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."}}