Figure 4.
The mapped locations on the GRCh38 reference sequence of Chicago read pairs are plotted in the vicinity of structural differences between GM12878 and the reference (A, deletion; B, inversion). Each Chicago pair is represented both above and below the diagonal. Above the diagonal, color indicates map quality score on the scale shown; below the diagonal, colors indicate the inferred haplotype phase of Chicago pairs based on overlap with phased SNPs, with read pairs of unknown haplotype origin shown in gray.
