{"id":"W2101342813","doi":"10.1101/gr.106344.110","title":"Detecting copy number variation with mated short reads","year":2010,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomic variations and chromosomal abnormalities","field":"Biochemistry, Genetics and Molecular Biology","cited_by":183,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto","funders":"","keywords":"Copy-number variation; Biology; Structural variation; Genome; Breakpoint; Computational biology; Reference genome; Human genome; Hybrid genome assembly; Copy number analysis; Genetics; DNA sequencing; Variation (astronomy); Identification (biology); Genomics; Gene; Chromosome","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007506215,0.00009793528,0.00008478928,0.00005706627,0.0002754504,0.00007873261,0.0001972577,0.0001418257,0.00035077],"category_scores_gemma":[0.00006261438,0.00008514019,0.00002820736,0.0001944387,0.00008468622,0.000005674854,0.0001225304,0.0003007989,0.0001161187],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002100067,"about_ca_system_score_gemma":0.0001534377,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001548545,"about_ca_topic_score_gemma":0.0001864031,"domain_scores_codex":[0.9988551,0.0000844231,0.000142748,0.0002873268,0.0002492918,0.0003811168],"domain_scores_gemma":[0.9991715,0.00001950326,0.00002401503,0.0003727176,0.0003232687,0.00008901836],"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":[0.0000661631,0.00003339293,0.01877736,0.00001447829,0.00004006617,0.00000442423,0.0001856087,0.00002796349,0.9797646,0.0004587931,0.00009748169,0.0005296392],"study_design_scores_gemma":[0.0009518104,0.0007964636,0.1859819,0.00001621353,0.00002893361,0.0003647593,0.001006025,0.0001546148,0.7290481,0.0006443957,0.08033069,0.0006759795],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9878771,0.00002284818,0.0007961032,0.00009956585,0.00007058151,0.0001827828,0.00001626993,0.00001727509,0.01091748],"genre_scores_gemma":[0.9944569,0.00002227021,0.002609082,0.00001960392,0.0003451673,0.00005054867,0.0001114276,0.00002505768,0.002359874],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2507165,"threshold_uncertainty_score":0.3840686,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02330027849323687,"score_gpt":0.3155932377844325,"score_spread":0.2922929592911957,"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."}}