Extended Data Fig. 3: ATAC–seq data summary.

a, The number of usable read pairs per tissue-stage, after filtering for mapping quality and PCR duplicates. b, The number of replicated ATAC–seq peaks called per tissue-stage. c, Genome coverage of replicated ATAC–seq peaks at each tissue-stage. d, Correlation of ATAC–seq signal at replicated peaks between biological replicates (n = 66 tissue-stages), as measured by Pearson’s correlation coefficient (left) or Spearman’s correlation coefficient (right). e, Multidimensional scaling (MDS) plot showing that the ATAC–seq signals at d-TACs tend to separate the samples first by tissue (indicated by coloured shapes) and then by stage (shade of colour within shapes). f, Fraction of usable reads overlapping TSS (measure of signal-to-noise ratio) for the ATAC–seq data and other reference data. H3K27ac ChIP–seq data and input from our ENCODE3 mouse tissues are shown to provide additional context for interpreting these numbers.