Overview of inversion discovery by paired-end mapping. The top part of the figure shows the alignment between the reference assembly and an individual carrying an inversion. When paired-end mapping is performed, the donor DNA is first sheared into several similarly sized DNA fragments. The ends of these fragments are then sequenced (fragments are depicted in blue and red, with the boxes at the ends showing the parts that are sequenced). The pairs of end-sequences are then mapped to the reference genome. The majority of these pairs will map in a plus(+)/minus(-) orientation, separated by the approximate distance expected from the fragment size (labeled A and D). End-pairs labeled B and C indicate mapping of fragment ends in a region containing an inversion compared to the reference assembly. Instead of the expected +/- orientation of the two end-sequences, the pairs spanning the inversion breakpoints map as +/+ and -/-, respectively. Clusters of such read pairs are indicative of an inversion. Only fragments spanning the inversion breakpoint will exhibit this pattern of alignment. Better clone coverage will yield better resolution and more accurate mapping of the breakpoints.