Extended Data Fig. 2: Genomic footprints are reproducible, overlap evolutionarily constrained nucleotides, and are enriched for TF recognition sequences.

a, Motif density is associated with footprint strength. Plotted is the overlap of motif recognition sequence matches (P < 0.0001) with nucleotides ranked by footprint P value from CD19⁺ B cells. b, As in a, but for per-nucleotide evolutionary conservation (phyloP). c, Scatter plot of per-nucleotide footprint P values for replicate experiments from the same cell line (NAMALWA Burkitt’s lymphoma cells). All individual nucleotides within FDR 1% footprints in either replicate were considered for correlation analysis. d, As in c, but for replicates of the same primary cell (CD8⁺ T cells) between two distinct individuals. e, Pearson’s correlation between replicates pairs grouped by whether they were derived from the same cell and individual (n = 43) or were the same primary cell or tissue from different individuals (n = 111). Boxes indicate median and inner quartile-range (IQR). Whiskers, 5th and 95th percentile.