Comparison of trend in first and second introns after controlling for their distance from the TSS. Using the start of first exon as a proxy for the TSS, distance from the first intron and the second intron to the TSS was obtained. Additional file 1: Figure S10A shows the length distribution of the two introns. Only the introns whose distance from TSS was in the overlapping range of 500–1000 bps were included in this analysis. Within this distance range, first and second introns were partitioned into smaller distance bins, and within each bin, various marks were compared between the first and the second introns. (A) Dark gray and light gray represent the proportions estimated in the first and the second intron respectively. (B) Table for the number of genes and corresponding statistics estimated by one-sided Wilcoxon rank sum tests for each comparison illustrated in (A).