Definition of breakpoints and breakpoint strings. For intra-chromosome rearrangements, four types of breakpoints - (a) null, (b) jump, (c) inverse and (d) repeat between genomic positions x and y - can be created that involve DNA on either the positive (red arrow) or the negative (blue arrow) strands. Edges are labeled with a number (for example, 3) representing confidence scores (for example, number of supporting reads) for the predicted adjacency. Edges without a number or with the number '0' represent reference adjacency (null breakpoints). For inter-chromosomal rearrangements, four possible novel alleles - (e) A-D, (f) B-C, (g) A-B and (h) C-D - can be created by joining four breakends (A, B, C, D) from two wild-type alleles (A-C, B-D) through genomic breakpoints x and y. Each allele can be represented in two different orientations involving combinations of either the positive (red arrow) or the negative (blue arrow) strands. (i) Breakpoint strings corresponding to the above configurations are listed, where '+' represents the positive strand and '-' the negative strand. The syntax of breakpoint strings is further explained in the Materials and methods.