Extended Data Fig. 6: Shared and genotype-specific peaks.

a, Percentage of TF diversity panel peaks also called as peaks in Mo17 (shared, grey) and those called only in B73v5 but not Mo17 (B73-specific, blue). b, Percentage of TF diversity panel peaks also called as peaks in B73 (shared, grey) and those called only in Mo17 but not B73 (Mo17-specific, green). Mo17 datasets show a similar percentage of Mo17-specific and Mo17-B73 shared peaks relative to those seen for B73-specific and B73-Mo17 shared peaks (TF order is same as in a). c, JBrowse2 genome browser view showing similar binding intensity of MADS69 in the 5’UTR of CYCLIN13 (Zm00001eb193830) in both genotypes. d, scatterplot showing good correlation of MADS69 reads in B73v5 compared to Mo17 MADS69 reads converted to B73v5 coordinates. e, JBrowse2 view of the MATE18 locus showing B73-specific peaks residing near a GWAS hit. Note that the B73-specific sequence insertion is not annotated as a TE. f, B73-specific peaks more often contain more than four SNPs per peak (top plot) or more SNPs per peak center (20 bp region surrounding the peak summit) (bottom plot). Shared peaks more often contain less than four SNPs per peak (top plot) or per the 20 bp region surrounding the peak summit (bottom plot). Data points represent individual TFs, n = 65. For f and g, whiskers indicate the minimum and maximum values; central lines correspond to medians and box boundaries denote the upper (25th percentile) and lower (75th percentile) quartiles. g, Overlap of B73-specific peaks and B73-Mo17 shared peaks with orthogonal datasets or DAP-CRMs. Both B73-specific peaks and shared peaks show statistically significant enrichment (p value < 0.0001, two-tailed t-test) relative to randomly shuffled peaks, providing support that both B73-specific peaks and shared peaks could be functional. Data points represent individual TFs, n = 200.