{"id":"W4414367040","doi":"10.5376/rgg.2025.16.0015","title":"Construction and Analysis of a Rice Pan-genome Reveals Structural Variation Hotspots Across Subspecies","year":2025,"lang":"en","type":"article","venue":"Rice Genomics and Genetics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"","keywords":"Subspecies; Structural variation; Variation (astronomy); Population structure; Population","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001689343,0.0003267932,0.0004210953,0.0006784604,0.0004037576,0.0002789528,0.0004259228,0.0002377126,0.002213304],"category_scores_gemma":[0.0002120282,0.0003204333,0.0007010077,0.0009452988,0.00018366,0.0002190415,0.000630238,0.000811192,0.0004411082],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003609784,"about_ca_system_score_gemma":0.0003333814,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002107134,"about_ca_topic_score_gemma":0.005409375,"domain_scores_codex":[0.9998622,0.00001223083,0.000008682292,0.00006854731,0.00001788646,0.00003040092],"domain_scores_gemma":[0.9997787,0.00005407574,0.0000385603,0.00003879504,0.00002204097,0.00006779184],"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":[0.0003074624,0.00002982139,0.001626769,0.00005154679,0.00002152256,0.00008987082,0.00007621304,0.0001774008,0.993928,0.0001496785,0.00004964255,0.003492001],"study_design_scores_gemma":[0.0001519384,0.0005753068,0.4679158,0.00003103436,0.0003609875,0.001547878,0.0004683273,0.005515074,0.5045775,0.0007459941,0.0180637,0.00004635723],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9757305,0.0002232228,0.01847188,0.00007810824,0.00001785086,0.0001026299,0.003303661,0.0002707536,0.00180134],"genre_scores_gemma":[0.9491148,0.0002576415,0.03224239,0.0001340156,0.00001261042,0.000138919,0.01501316,0.000284404,0.00280212],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002213304,"threshold_uncertainty_score":0.007404208,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007282872778838143,"score_gpt":0.2490404758101139,"score_spread":0.2417576030312757,"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."}}