Table 1.

Quality control metrics

QC Metric	Information gained from this metric
Read metrics	Number of mapped and unmapped reads
CpG Coverage	Number of CpGs observed with a minimum coverage threshold
M-bias	Average methylation by position across reads. Deviation from uniformity typically indicates a problem with library construction or data preprocessing.
Downsampling saturation curve	CpG coverage as a function of number of reads. A rising curve indicates that we would expect to observe additional CpGs from deeper sequencing of a library
CpG discretization	Useful in single-cell analysis, this represents the fraction of CpGs with non-binary methylation status
Feature level coverage	The fraction of key genomic features (e.g. promoters, CpG Islands), covered with at least 1 CpG.
Bisulfite conversion rate	The proportion of non CpG context C’s that were converted to T. This should be close to 100% in most mammalian tissues.
CpG density distribution	The CpG density distribution around observed CpGs is typically similar across samples indicating coverage of similar genomic regions.
Methylation distribution	Unexpected sample-to-sample deviations in the distribution of methylation values can indicate potential technical artifacts