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. 2017 Oct;27(10):1704–1714. doi: 10.1101/gr.212373.116

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© 2017 King 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 1. — Detecting structural mosaicism using MrMosaic. (A) Exome data are stored in a BAM file from which allele fraction (left) and coverage (right) are measured at polymorphic positions within or near target regions. A simulated mosaic deletion is depicted. (B) The raw data, consisting of BAFs (y-axis: B allele frequency) and normalized coverage (y-axis: log ratio of normalized coverage) are plotted across chromosome space (x-axis) for a simulated mosaic deletion. (C) Absolute deviation of BAF (y-axis: B_dev) and normalized coverage (y-axis: C_dev) at heterozygous sites are analyzed. A smoothed median has been included. (D) Mann-Whitney U tests were performed separately for B_dev and C_dev, comparing the signal detected in sliding windows in this chromosome compared with randomly selected sites from other chromosomes, generating a test statistic (y-axis). A smoothed median has been included. (E) The test statistics are depicted in log scale. The P-values of the Mann-Whitney U tests were combined and segmented (black lines). Segments passing the Mscore significance threshold are plotted in blue.