{"id":"W4361018486","doi":"10.1101/gr.277372.122","title":"A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes","year":2023,"lang":"en","type":"article","venue":"Genome Research","topic":"Genetic and phenotypic traits in livestock","field":"Biochemistry, Genetics and Molecular Biology","cited_by":117,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"National Key Research and Development Program of China; China Postdoctoral Science Foundation; National Natural Science Foundation of China","keywords":"Biology; Genetics; Linkage disequilibrium; Single-nucleotide polymorphism; SNP; SNP genotyping; Phenotype; Allele; Structural variation; Population; Indel; Haplotype; Genome; Evolutionary biology; Gene; Genotype","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":[0.0006044979,0.0004385986,0.000547244,0.001215252,0.0003851844,0.000551763,0.000194167,0.0004430058,0.001223026],"category_scores_gemma":[0.001258416,0.0002792373,0.0006989817,0.001406255,0.0001483995,0.0003629764,0.0006319818,0.000585864,0.000571311],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001378135,"about_ca_system_score_gemma":0.0002362257,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009999864,"about_ca_topic_score_gemma":0.002619574,"domain_scores_codex":[0.9996601,0.00004391238,0.00003774741,0.0001514251,0.00007382033,0.0000330104],"domain_scores_gemma":[0.9992636,0.0002667835,0.0001542798,0.0001001841,0.0001312172,0.00008390393],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.0005908621,0.00006450697,0.100214,0.0008617152,0.0005317837,0.0007759894,0.0009223829,0.001571181,0.8397216,0.0004430715,0.002132078,0.05217088],"study_design_scores_gemma":[0.00005103552,0.0003599398,0.9177455,0.0001591813,0.0006653973,0.00252849,0.0003790631,0.005852376,0.03854364,0.000829952,0.03281867,0.00006672634],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9436985,0.002599949,0.01974449,0.0001323153,0.00003445815,0.00005829836,0.0315402,0.0005191376,0.00167258],"genre_scores_gemma":[0.8065272,0.002261852,0.05613345,0.000209781,0.00004461922,0.000185116,0.1322813,0.0006603315,0.001696293],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001223026,"threshold_uncertainty_score":0.004091442,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0287817908418471,"score_gpt":0.3043156987600525,"score_spread":0.2755339079182054,"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."}}