Extended Data Fig. 5.

Schematic of read-pair mapping signatures for a small dispersed DUP and a divergent reference repeat. Locus ‘A’ is duplicated in the donor genome. Some read pairs map discordantly in the RL orientation (green) or with a large insert size (red). Pairs internal to each copy of the donor map to the single copy of ‘A’ in the reference genome, doubling its coverage. If the reference has a divergent copy of ‘A’ (denoted as ‘a’), a gap in coverage will be observed at ‘a’.