Fig. 2

Tv’s are depleted at TF binding sites. a, b Changes to PWM scores for JASPAR TFs caused by Ts’s (grey boxplots) and Tv’s (white boxplots) ordered by normalized position (above) and information content (below). For each position in each consensus sequence, we calculated the position specific scoring matrix (PSSM) score of having every possible nucleotide at that position and, subsequently, the change in PSSM score when mutating any nucleotide to any other nucleotide at that position. Black squares are changes >1.5× above the interquartile range. P-values for parameter estimates were calculated using a t test, and are reported without adjustment for multiple hypothesis testing. We tested 11 and 20 hypotheses in Fig. 2a and b, respectively. Applying a Bonferroni correction to a nominal p-value threshold of α = 0.05 gives a significance threshold of α = 0.005 and α = 0.0025 for 2A and 2B, respectively