Linkage between fragment size and local DNA methylation in non-pregnant ccf DNA. (a) Fragment size of ccf DNA as measured by WGBS. Each line represents an individual ccf sample. Loss of representation at approximately 92 to 98 bp is an artifact of adapter trimming prior to alignment. (b) Ratio of methylated CpG, CHG, and CHH cytosines within large fragments (>200 bp) relative to methylated cytosines in small fragments (<200 bp) after scaling for number of cytosines measured. Each bar represents a single sample. (c) Size distribution of unmethylated fraction (black) and methylated fraction (gray) using MCIp-Seq. Each line represents an individual sample fraction. Inset plot provides a quantified distribution of fragment size for each fraction.