Extended Data Fig. 4: Inverted repeats and segmental duplications.
From: Chromosomal inversion polymorphisms shape the genomic landscape of deer mice
Examples of inversion breakpoints near large inverted repeats (inv9.0, inv15.2, inv20.0) and segmental duplications (inv9.0, inv15.2, inv20.0, inv18.0). Dotplots show alignments for long-read assembly contigs spanning or nearly spanning breakpoints. Self-v-self alignments are highlighted (gray boxes), with alignments between breakpoint regions (within 500 kb of breakpoints) shown in upper left quadrant for inv9.0, inv15.2 and inv20.0. Location of breakpoints (red arrows) shown; only alignments with length >100 bp and within 500 kb of the breakpoints are shown. Inverted repeats mapping to within 500 kb of both breakpoints are shown (red) and highlighted (yellow boxes). Self-v-self alignments also show segmental duplications near breakpoints.
