Fig. 2.

—(A) Reads from the newly sequenced genome are mapped to the reference genome. Reads from the parental gene will map well (Set 1). Read from the retroCNV will not map well (Sets 2–4). They will hit the region of the parental region but there will be problems: reads spanning exon–exon junctions (Set 2), pair reads mapping farther apart than expected from de sequencing protocol (Set 3), and discordant reads (i.e., reads mapping to different regions in the genome; Set 4). (B) The reads that do not map well can be used to assemble the retroCNV.