Fig. 5

High false discovery rates of intrahost variants using Nanopore sequencing. a iSNV false discovery rates (FDR) from Oxford Nanopore sequencing data. We analyzed 54 true positive and 4173 true negative sites, and determined the proportion of true and false positive iSNV calls from datasets containing 1, 2, or 3 technical replicates using either a 3% frequency cutoff or a logistic regression of iSNV frequency and strand bias. b A receiver operator characteristic (ROC) curve showing a logistic regression model that incorporates allele frequency and strand bias as features and the presence or absence of a iSNV as the response variable. The model was trained and tested using a 10-fold cross validation scheme. The model was performed using a frequency and strand bias threshold alone, and combining the two features. Post-filter iSNV frequencies of true and false positive calls using c a 3% cutoff or d a logistic regression of iSNV frequency and strand bias. Data shown as the means and 95% confidence intervals