Fig. 3

Impact of VAF cutoff, variant type, and genomic region on sensitivity (in Phred scale). a Violin distribution plots of estimated sensitivity for each panel in all sample A and C libraries for known SNVs (in blue on the left side) and other variants (small indels or MNVs, in green on the adjacent right side) with VAF between 2.5 and 20%. Total numbers of small indels and MNVs are listed under the corresponding violin plot. b Artificial VAF filters reduce sensitivity for known positives with VAF between 2.5 and 5% due to the variable VAF measurements. c High concordance of sensitivity in and outside of CTR (more specifically, in HC_CR beyond CTR) for known positives with VAF between 2.5 and 20%. Jittering was applied to one dot at the top right corner to avoid overlapping