Call-rate matrix, which contains the rate at which six-letter seq calls unmodC, 5mC and 5hmC when the true state is unmodC, 5mC and 5hmC. This is estimated from ground-truth control sequences for which the modification status of each CpG is known. We calculate the rate at which six-letter seq calls unmodC, 5mC and 5hmC at unmodCpGs on a fully unmethylated pUC19 (first column), the rate at which six-letter seq calls unmodC, 5mC and 5hmC at 5mCpGs on a fully methylated lambda genome (second column), and the rate at which six-letter seq calls unmodC, 5mC and 5hmC at 5hmCpGs on a synthetic oligonucleotide (third column).
