2026-10-12T01:55:18Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34074146 2026-10-05T17:57:29Z category_4 category_13 category_14 category_21 category_24 category_734 category_931 category_64 category_132 category_134 portal_5 item_type_3 month_year_10_2026

<p>Recall and false discovery rates for variants at 5%, 10%, 15%, and 19% frequencies across Phred score scalar adjustments. Plasmid truth sets normalised to 2,000 × depth (n = 12 subsampling replicates per condition; df = 11, t-critical = 2.201). The Control row is a technical duplicate of the Uncalibrated condition, confirmed by identical VCF hash signatures. Phred score reduction removes all false positives at −8 on both chemistries. Variants at 15% AF and below are adversely affected by Phred reduction on R9.4.1 flow cells, while only 5% AF variants are affected on R10.4.1 flow cells. CI = 95% confidence interval; FDR = false discovery rate.</p> Xavier Zair (25317383) Andreas Wilm (7951) Miles C. Benton (9601012) Cheng Yong Tham (8528523) Lin Yang (45852) Paola Florez de Sessions (9048782) October Michael Sessions (6635093) Eng Hui Chew (25317386) Swapnil Mishra (8611860) Biochemistry Genetics Molecular Biology Biotechnology Evolutionary Biology Biological Sciences not elsewhere classified Information Systems not elsewhere classified Cancer Infectious Diseases Virology widely used caller tracking viral evolution sequenced using r9 oxford nanopore technologies false discovery rates benchmarked across chemistries consensus variant calling lofreq &# 8217 xlink "> next 1 flow cells xlink "> lofreq xlink "> consensus variants study assesses short reads library sizes less effective haploid genomes generation sequencing effective sequencing detecting variants best performance also introduced 7179 bases 100 snvs <p>Recall and false discovery rates for variants at 5%, 10%, 15%, and 19% frequencies across Phred score scalar adjustments. Plasmid truth sets normalised to 2,000 × depth (n = 12 subsampling replicates per condition; df = 11, t-critical = 2.201). The Control row is a technical duplicate of the Uncalibrated condition, confirmed by identical VCF hash signatures. Phred score reduction removes all false positives at −8 on both chemistries. Variants at 15% AF and below are adversely affected by Phred reduction on R9.4.1 flow cells, while only 5% AF variants are affected on R10.4.1 flow cells. CI = 95% confidence interval; FDR = false discovery rate.</p> 2026-10-05T17:57:18Z Dataset Dataset 10.1371/journal.pone.0356259.t001 https://figshare.com/articles/dataset/_p_Recall_and_false_discovery_rates_for_variants_at_5_10_15_and_19_frequencies_across_Phred_score_scalar_adjustments_Plasmid_truth_sets_normalised_to_2_000_depth_n_12_subsampling_replicates_per_condition_df_11_t-critical_2_201_The_Control_r/34074146 CC BY 4.0