Predicting structural variation from new junction and missing coverage evidence. a) Types of structural variation for which breseq can predict precise mutational events from new junction sequences (JC) and missing read coverage (MC) evidence are shown in the context of the reference and mutant genomes. For JC evidence, the matched sequence on each side is shown as a solid arrow with a dashed line connecting the two sides. Orange JC arrows indicate that this side of a new sequence junction maps equally well to multiple locations in the reference genome (i.e., the location is ambiguous). Details for the procedure used in each case are described in the text. b) Mobile element insertions may require additional fields to describe the precise sequence change caused by insertion of a new copy. These may include a target site duplication and deleted or inserted bases on the margins of the new element copy, as shown.