ssDNA hotspots, paternal crossing over events and East Asian ancestry (EAS) haplotype blocks were intersected with chromatin loops in early primary spermatocytes (from EAS sample donors). In each row, the first plots show average enrichment scores across all loops (plus/minus 20% of loop length), including, as shaded bands, the standard error of the mean and the 95% confidence interval for the mean. The second plot in each row is a probability density plot based on 1000 circular permutations; the observed number of overlaps between loop anchors and ssDNA peaks, paternal crossing over events and EAS haplotype blocks is indicated by the green vertical lines; in each case the expected distribution of overlap is shown as a grey histogram. The threshold for statistical significance is indicated by the red vertical lines. The last plot in each row shows the distribution of shifted Z -scores, i.e. the variation in circular permutation Z -scores if loop anchors and ssDNA peaks, paternal crossing over events or EAS haplotype blocks, respectively, were shifted with respect to each other. A distinct peak (or trough) in the local Z -scores indicates that overlaps result from specific local patterns.
