Fig. 2

Illustration of the effect of a NAHR mediated inversion on long read sub-alignments. Idealised NAHR inversion and reference are shown in first two panels. Inverted repeats are shown as dark and light blue. Orange, dark purple and blue hashed rectangles indicate unique sequence. The direction of the hashing indicates its orientation. The third panel (red) shows a read supporting the left breakpoint of the inversion. The large arrow indicates the original unmapped read. The smaller arrows indicate two sub-read alignments, with the direction of the arrow indicating the alignment orientation, and the horizontal dashed line indicating aligned and clipped sequence. The dot lines indicate the position of the subread alignment on the original read. The fourth panel (green) is similar to the third panel, except that it illustrates the read supporting the right breakpoint