Summary of structural variation between chimpanzee and human. A diagram of the location of all 651 structural variants between humans and chimpanzee mapped to the human reference assembly. Chimpanzee deletions (n = 293) are shown in red; insertions (n = 184) are shown in blue. Inversions/duplicative transpositions (n = 174) are classified into three groups: confirmed pericentric cytogenetic inversions from Yunis and Prakash (1982) (orange); double breakpoint inversions, if both of the breakpoints were captured (green); and single breakpoint inversions, if only one end was captured (gray). A significant fraction of the latter corresponds to duplicative transpositions of segmental duplications as opposed to bona fide inversions. The complete coordinate list for all sites of structural variants is provided in Supplemental Table 1. Supplemental Figures 3–26 provide a detailed map of all variation at the kb level for each chromosome.