Figure 2

Size and significance of the effect of AluY insertions on the local recombination rate. (A) The effect of AluY insertions (linear regression coefficient for the AluY variable) is plotted against the percent divergence of AluY elements (binned into non-overlapping groups of approximately uniform number, i.e., 600-800 elements; divergences taken from RepeatMasker). The red and black lines correspond to results from the HapMap YRI and CEU data sets, respectively. (B) Histogram of AluY element frequencies vs. percent divergence from their respective subfamily consensus sequences. Only elements between 250 and 350 bp long, with no more than 10% of their sequence deleted or composed of non-Alu insertions, were counted. The dark gray histogram shows the distribution of AluY elements that were chosen for regions analyzed in this work (magnified vertically by fivefold for visibility), while the light gray histogram includes all AluY elements. The horizontal axes in both panels are identically scaled and aligned.