Fig. 2

Issues can arise in the second mapping step of ISMapper if the IS insertion is next to a region that occurs more than once in the reference genome. In this example, the left flanking reads (green arrows) have mapped to all possible copies of the repeat sequence (dark red boxes) and are each randomly assigned to a repeat copy by BWA, resulting in each copy falling below the read depth cut-off (default 6x). To overcome this, where an unpaired flanking region is identified (purple box), ISMapper searches for a potential low-depth partner flanking region that is close to or intersecting the confident region (green box). This is recorded as an uncertain call, labelled in the output with the ‘?’ character