Fig. 3

The consequence of ‘missingness’ in RRBS data demonstrated by array and simulation bisulfite-sequencing data. A) A boxplot showing the proportion of DNAm points that have ‘extreme’ DNAm (0.05 < DNAm < 0.95) calculated for DNAm points with different read depths (x axis). B) Violin plots showing the distribution of estimated DNAm values from a simulated bisulfite sequencing experiment for a DNAm site where the true value is 0.50, as a function of read depth. Line graphs showing the Pearson correlation (Ci) and root mean squared error (RMSE) (Cii) between simulated and ‘real’ DNAm values for 1000 DNAm points as a function of read depth. These analyses used a subset of real data selected to contain DNAm points with read depth > 10 and evenly distributed DNAm (see Methods). Scatterplots of DNAm values quantified using RRBS (x-axis) and a custom vertebrate Illumina DNAm array [30] (y-axis) in matched samples (n = 80) for D) all DNAm points and E) the subset of DNAm points with read depth greater than the peak Pearson correlation read depth in Fi (i.e. 22 reads). Line graphs showing Fi) the Pearson correlation and Fii) error (RMSE) of RRBS data and array data as a function of the read depth filter applied to the RRBS dataset