e9.5 UR domains characteristics.

<p><b>A</b>. UR domain size and depletion are correlated. Plot of size (0–8,500 kb) versus percent chromosomal median depletion (25–60%) of UR domains. <b>B</b>. UR domains are found using two different platforms: aCGH and WGS, although the calculated degree of underrepresentation is increased using WGS. Plot comparing position along chromosome 14 to the NLog2 Ratio of array intensity (aCGH) and sequence coverage (WGS) of TGCs vs. embryos. Red: e9.5 WGS; blue: e9.5 aCGH. Two biological replicates are plotted for each platform (LitterA shown for WGS). All autosomes shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004290#pgen.1004290.s004" target="_blank">Figure S4</a>. <b>C</b>. Individuals with a lesser number of UR domains have a subset of the UR domains found in the samples with a greater number of UR domains. Venn diagram showing UR domain overlap between six individuals from three separate litters (A, B and C). <b>D</b>. UR domains among individuals are nested. Plot comparing position along the last half of chromosome 14 to the NLog2 Ratio of sequence coverage of TGCs vs. embryos. Color code the same as in (<b>B</b>). Dashed line: cut-off for significance. All autosomes shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004290#pgen.1004290.s005" target="_blank">Figure S5</a>.</p>