Fig. 3. Alignment-based and assembly-based SV discovery.

a SV discovery recall and precision of alignment-based SV callers when compared with the assembly-based SV callset. b SV breakpoint accuracy of DeBreak, pbsv, cuteSV, and Sniffles in PacBio CLR (top) and HiFi (bottom) datasets. c Venn diagram showing the overlap among four SV callsets. The number of SV events in each category is labeled within each section. d Distribution of PAV-unique and DeBreak-unique SV calls on chromosomes 1–5. Red boxes indicate the positions of centromeres. Source data are provided as a Source Data file.