Fig. 4

Structural variants from SMRT-SV v2 [5]. The pseudodiploid genome built from two CHM cell lines and one negative control sample was originally used to train SMRT-SV v2 Genotyper in Audano et al. [5]. It contains 16,180 SVs. The SVPOP panel shows the combined results for the HG00514, HG00733, and NA19240 individuals, three of the 15 individuals used to generate the high-quality SV catalog in Audano et al. [5]. Here, we report the maximum F1 score (y-axis) for each method (color), across the whole genome or focusing on non-repeat regions (x-axis). We evaluated the ability to predict the presence of an SV (transparent bars) and the exact genotype (solid bars). Genotype information is not available in the SVPOP catalog hence genotyping performance could not be evaluated