(a–d) A simple breakpoint in sarcoma sample 0. (e–h) Two breakpoints in close proximity in sarcoma sample 0. (a,e) Heat maps indicate barcode similarity for each pair of genomic locations. In a, the greatest signal forms a corner at the breakpoint coordinates. In e, two breakpoints can be discerned by a dropoff in signal at 108.85 mb (x-axis) in addition to 93.27 Mb and 93.25 Mb (y-axis). (b,f) The same region from a and e in the control sample. (c,g) Inferred extent of breakpoint-supporting read clouds (corresponding to input fragments). Each row is one cloud, colored according to its assignment to a haplotype; supporting haplotype, orange; unassigned, black; nonsupporting haplotype, cyan; and nonsupporting cloud in the same barcode as a supporting cloud, gray (derived from independent fragments in the same molecular partition). The long fragments tile across the breakpoint when ordered by their leftmost position in the left panel. (d,h) Copy number profiles based on the short-fragment data in the sarcoma. Decreasing coordinates depict the minus strand.