{"id":"W4238138425","doi":"10.7287/peerj.6995v0.1/reviews/1","title":"Peer Review #1 of \"ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data (v0.1)\"","year":2019,"lang":"en","type":"peer-review","venue":"","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Food Inspection Agency","funders":"","keywords":"Contamination; Biology; Whole genome sequencing; Computational biology; Genome; Sequence (biology); Genetics; Gene; Ecology","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0182346,0.001413646,0.002325015,0.007536434,0.005446585,0.009135788,0.003481945,0.00325234,0.4204122],"category_scores_gemma":[0.1603846,0.0008774846,0.001823765,0.002933165,0.002278235,0.00556865,0.00828199,0.002450445,0.3121298],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.002050222,"about_ca_system_score_gemma":0.01447942,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004412323,"about_ca_topic_score_gemma":0.01126169,"domain_scores_codex":[0.9770758,0.004043566,0.002574014,0.001711213,0.01331694,0.001278434],"domain_scores_gemma":[0.7134642,0.02542189,0.005746099,0.01420493,0.2227801,0.01838275],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00003532438,0.0000152859,0.0002762493,0.0006583275,0.00001768872,0.0001333666,0.0001206133,0.00005200972,0.0004325198,0.0004974034,0.9629291,0.03483197],"study_design_scores_gemma":[0.00003042692,0.00001661402,0.0007172201,0.0003387903,0.0000180191,0.000136601,0.0001483323,0.0003308951,0.0008015336,0.0009427636,0.9964832,0.00003559022],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"editorial","genre_gemma":"other","genre_scores_codex":[0.007057066,0.007846372,0.03664387,0.1381025,0.4379704,0.01238705,0.0419481,0.02449107,0.2935535],"genre_scores_gemma":[0.03308253,0.008165743,0.03337116,0.01088935,0.05529269,0.003505871,0.042252,0.01966824,0.7937724],"genre_candidate":"other","genre_consensus":null,"teacher_disagreement_score":0.4204122,"threshold_uncertainty_score":0.8267117,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0605040994624655,"score_gpt":0.3177006034107069,"score_spread":0.2571965039482415,"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."}}