Fig 2. Different orientations of alignment pairs.

Each pair consists of two alignments of the same read. The first alignment is marked as the one that involves the left-most part of the read and the second alignment as the one that involves the right-most part of the read. The first alignment is highlighted in blue and the second is highlighted in yellow. If the first alignment has mapped the read to a position in the subject preceding the second alignment, then the pair, as well as the read that covers the junction, is of forward orientation. In the opposite case, the pair, as well as the read that covers the junction, is of reverse complement orientation. When both the first and the second alignment are of forward orientation (A), the pair corresponds to a deletion when the pair itself is of forward orientation. The pair describes a deletion again when both alignment and the pair itself is of reverse orientation (A). Similarly, different combinations of each alignment orientation and their symmetric reverse complement of the pair are described for 3’copy-back (B), 5’ copy-back (C) and insertion of duplicated sequence (D). The grey vertical lines denote the location of the decided breakpoint on the read in case of multiple solutions of the maximum score path.