Extended Data Fig. 7: SV breakpoint homology and microhomology landscape separated by SV annotation.

For all SVs, homology and microhomology was determined. SVs were annotated using the SVAN pipeline as well as by leveraging flanking repeat elements and/or homologous sequence stretches. SVs were grouped into a) repeat-mediated SVs, b) segmental duplication (SD)-mediated SVs, c) duplications (DUP), d) mobile elements (MEI), e) VNTRs, f) not-classified (NA) or NHEJ-mediated SVs. The central scatter plot shows SV length versus (micro)homology length, for each group. Marginal histograms show the distribution of SV length (top) and homology length for deletions (left) and insertions (right). The axes are linear from 0 to 50 bp and log-scale afterwards, which is denoted by a dashed line. To highlight the distribution of rare SV classes, the stacking order in the marginal histograms proceeds from rare (bottom) to common classes (top). Colors correspond to those used in Fig. 5.