Extended Data Fig. 5: Quality assessment of B73 and Mo17 DAP-seq datasets.
From: Transcription factor binding divergence drives transcriptional and phenotypic variation in maize
a, Pearson correlation of TF binding profiles for B73 and Mo17 genomes. Most B73 peak datasets (rows annotated in yellow) clustered with Mo17 peak datasets for the same TFs lifted to B73 (rows annotated in teal), as indicated by the magenta boxes. b, Percentage of non-crossmappable peaks (coordinates could not be lifted) that overlapped with “Non-Alignable” region (NotAligned), duplicated regions (DUP), or structural variants (SV, insertions or deletions greater than 50 bp). Each datapoint corresponds to the percentage of peaks from an individual TF overlapping the indicated category, n = 200. Whiskers in boxplots in panels b-d indicate the minimum and maximum values; central lines correspond to medians and box boundaries denote the upper (25th percentile) and lower (75th percentile) quartiles with n = 200 TFs. c, Upper: scatterplots showing no difference in average reads per peak or percentage of peaks with motif for shared and specific datasets. Each dot corresponds to a single TF. Lower: distribution of average reads per peak and percentage of peaks with motif for shared and specific datasets. n = 66 d, Percentage of peaks within each category that overlapped SVs and transposable elements (TEs), n = 200.
