Fig. 3

The figure displays the basic design of our approach for SV calling using an example. A The dot-plot diagrammatically visualizes an inversion of section ‘B’ on the sequenced genome. This inversion induces one breakend pair on the reference genome and one breakend pair on the sequenced genome. B shows the dot-plot of A unfolded into the forward strand and reverse strand. There are two reads \({r}_{1}\) and \({r}_{2}\), where \({r}_{1}\) originates from the forward strand and \({r}_{2}\) originates from the reverse strand of the sequenced genome. The locations of both reads on the sequenced genome (right) and the reference genome (top) are visualized, where the reads decompose into two segments on the reference genome. The reads indicate the inversion’s breakend pairs, once on the forward strand via the arrow labeled “a” and once on the reverse strand via the arrow labeled “b.” C The inversion’s breakend pairs are visualized in a corresponding adjacency matrix via the matrix entries labeled “a” and “b.” The x-position of an entry (breakend pair) is the origin position on the reference, while the y-position corresponds to the destination position. D We apply our matrix folding scheme to the adjacency matrix of subfigure C for unifying breakend-pair calls (matrix entries) from forward and reverse strand reads. E shows the genome mapping graph defined by the adjacency matrices of C and D