Summary of the characteristics of the analyzed inversion predictions and iPCR validation results.

1<p>Inversion size is calculated as the distance between the middle positions of the two breakpoint intervals.</p>2<p>Consistency between the iPCR and paired-end mapping (PEM) results is indicated by the number of individuals in which the iPCR genotype is consistent with the presence of fosmids supporting the <i>Std</i> or <i>Inv</i> orientation after excluding those mapping within the IRs (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004208#pgen.1004208.s005" target="_blank">Table S2</a>).</p>3<p>HsInv0306 includes this inversion prediction and HsInv0312, whereas HsInv0710 includes this inversion prediction and HsInv0311 <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004208#pgen.1004208-MartnezFundichely1" target="_blank">[54]</a>.</p>4<p>The inverted region of inversion HsInv0403 shows the opposite orientation in the GRCh37 (HG19) assembly.</p>5<p>For inversion predictions in which no inverted sequence was available, breakpoint coordinates correspond to the whole length of the segmental duplications (SDs) annotated in HG18 or the IRs defined by BLAST alignment of the two breakpoints.</p>6<p>IRs include sequences of transposable elements (TEs) L2, MLT1K, MLT1C, AluSq, L3, and MIRb, although the whole region has been anotated as SD in HG19.</p>7<p>IRs are annotated as SDs in HG18, but not in HG19 since they are completely formed by multiple partial copies of different TEs.</p>8<p>IRs are not annotated as SDs in HG18 or HG19, but contain unique sequences and parts of different TEs (L2, L4, MER41C, MER4A, and MamGyp).