Fig 3. Distinguishing simulated events from background mutation clusters and setting alignment quality thresholds.

(A) Percentage of events recaptured from simulations of template switch events alongside substitutions and indels using INDELible across a range of divergences. (B) Receiver operating characteristic (ROC) curves for discriminating between simulated template switch events and background mutation clusters. Simulations using divergence t from 1–2% in 0.1% steps are shown (t value for each curve indicated by matching colour in part A). Note that the y-axis begins at 0.95 for clarity. (C) Density curves of LPRs for true positive (i.e. intentionally introduced) template switch events in colours corresponding to (A), and false positive events across all simulation values of t (background/chance mutation clusters) in grey. The mean LPR threshold required to achieve a FPR of 0.005 across simulations is shown as a dashed line.