(A) The global plot of gene density, Rmap with a k-mer length of 20 (Rmap20) and repeat density (from outer to inner) in the human genome. A local view in chr3: 161 343 500–161 374 900 is shown on the right. Circos [63] and IGV [64] were used to draw the plot. The gene annotation was downloaded from GENCODE. The repeats were annotated by RepeatMasker. (B) The scatter plot shows the low correlation between gene density and repeat density (cor = 0.08, p = 3.3e-06). Here, the human genome is segmented into 3102 1 Mbp fragments. The gene density and repeat density are the ratios of gene region and repeat region in each fragment, respectively. (C) The figure shows a positive correlation between gene density and sequence repetitiveness (cor = 0.51, p < 2.2e-16). The rscore values are log normalized and scaled for easy comparison. (D) The normalized repetitive scores on gene regions and random regions in the human genome. The random regions are generated by shuffling the gene set (shown in dark blue). The repetitiveness profiles across the coding genes and LncRNA genes are shown in light blue and yellow, respectively. The deepTools [65] is used to draw this plot.