and Del (inversion with adjacent deletion; n = 9) and ‘MultiDel’—a class where two or more adjacent deletions are separated by at least one sequence ‘spacer’ of up to ∼204 bp in length (n = 370). However, not all complex SVs fit into these classes, with 214 sites forming distinct patterns corresponding to multiple classes or exhibiting increased complexity. Template-switching mechanisms could explain the notable complexity of these SVs3. Indeed, microhomology patterns were typically present between the breakpoints of deletions and the respective boundaries of insertion templates at these sites (Extended Data Fig. 9), consistent with formation through single mutational events (Supplementary Note). Across the complex sites assessed, 871 (53%) showed evidence for a local template (≥10 bp match, within 10 kbp), whereas for 41 the insertion was presumably templated from a distal region (≥22 bp match, >10 kbp away), including 17 sites where the DNA stretch was likely derived from RNA templates (Supplementary Table 13).
