Figure 3.

Small variants accumulate at differential SV breakpoints. (A) SV insertions with different breakpoints (blue) in each haplotype pair were retrieved. Sequence around the left and right breakpoints was extracted (solid box) for both haplotypes including the differential locus (gray area between dashed lines) and 50 bp upstream and downstream. The red dashed line on the right side of each gray box marks the start and end position of the right-shifted variant. (B) Small variants accumulate at the upstream and downstream edges of the right-shifted variants where zero is the red line in A. Small polymorphisms occur most frequently 1 bp inside the right-shifted insertion sequence (red arrow).