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. 2016 Mar;26(3):342–350. doi: 10.1101/gr.193474.115

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© 2016 Putnam et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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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.