Signals of structural variation from paired-end sequencing. (a) Fragments (black arches) from a test genome are sequenced from both ends and the resulting paired reads are mapped to a reference genome. Fragments containing the breakpoint of a structural variant (black arches with arrows) have a discordant mapping (red). (b) The GASV program  efficiently clusters discordant fragments supporting the same variant and provides precise information about the localization of the adjacency, (a,b), created by the rearrangement. For example, on the left a deletion of the interval from the reference creates a novel adjacency of breakends and . GASV represents the novel adjacency as a breakend polygon (shaded red trapezoid) where the left and right breakends of the variant must lie within the breakend polygon. In this example, we show breakend polygons for a deletion (left) and an inversion (right), each supported by two discordant fragments. (c) The presence of a structural variant is also indicated by changes in the depth of coverage of concordant mappings. For the deletion (left) the depth of coverage is low throughout the entire region, while for the inversion (right) the depth of coverage drops only near the breakends.