Fig. 7

The genomic patterns of SSB hotspots near TSSs differ from those of AP site hotspots. (A) Violin plot distributions of the TSS-SSBs enrichment ratios (Y-axes) for the sample-shared SSB (pink) or AP site (green) hotspots (depth ≥ 1) in six tissues. Individual data points are shown. (B) Box plots of the odds ratios (Y-axes) of enrichment of sample-shared SSB or AP hotspots (depth ≥ 1) found on other template or non-template strands in the indicated (X-axis) non-overlapping distance bins to TSSs in the different tissues. (C) Template vs. nontemplate ratios (Y-axes) of sample-shared SSB or AP hotspots (depth ≥ 1) in each indicated (X-axis) distance bin and each tissue. (B, C) Green represents bone marrow, light blue represents heart, light green represents PBMC, orange represents brain, pink represents liver and yellow represents sperm. The asterisks above the horizontal lines denote the significance of the difference: *, ** represent respectively p-values < 0.05 and 0.01 (Wilcoxon Rank Sum Test), while “ns” mean no significant difference. Box plots indicate median (middle line), 25th, 75th percentile (box) and 1.5× interquartile range (whiskers) as well as individual data points. (D) The difference in the sequence compositions around TSSs that contain AP site hotpots within ± 5 bp vs. those that contain SSB hotspots within the same range on either template or non-template strand. Only bases with differences > 0.05 (5%, Y-axes) at each position are shown. Positive values on Y-axes indicate enrichment in the TSSs with the AP site hotspots. The TSSs are highlighted