Calculation of bisulfite conversion rate

Bisulfite treatment involves converting cytosine to uracil while leaving 5-methylcytosine (5-mC) intact. Therefore, bisulfite conversion rates can be measured by mapping reads to the chloroplast genome, which is unmethylated, since we know that here all cytosines should be converted to uracil (Fojtová et al. 2001; Lister et al. 2008). While we did not enrich for chloroplast DNA, because we used total wheat DNA, a proportion of our off-target sequences mapped to the wheat chloroplast genome. The off-target DNA was mapped to an average of 66.5% of the chloroplast genome across all accessions to 406× per accession (Supplemental Table S3).