Two DNA controls are provided: unmethylated lambda DNA and 5hmC T4 DNA. 5hmC T4 DNA is hydroxymethylated in the CpG, CHG and CHH contexts. For unmethylated lambda DNA, less than 1% hydroxymethylation is typically observed indicating a conversion efficiency of greater than 99%. For 5hmC T4 DNA (all cytosines are hydroxymethylated), greater than 96% 5hmC is typically detected in all three cytosine sequence contexts.