Microhomology analysis
To determine the extent to which microhomologies are associated with deletion variants, we used MHcut(Grajcarek et al., 2019) to search for homologous sequences at the junction sequences of deletion variants, thereby yielding a score with which to evaluate any microhomology present. For each deletion entry, microhomology was tested for both flanking configurations (5′ flanking region with 3′ variant sequence and 3′ flanking region with 5′ variant sequence), from which we selected the one with the highest score. The enrichment of microhomologies in the flanking sequence of deletions was assessed by means of the Chi-square test.