Differential jagged ends between fetal and maternal DNA molecules revealed by the incorporation of methylation at CH sites. (A) Methylation level at CH sites in the relative positions of read1 and read2 for shared and fetal-specific DNA molecules. (B) Averaged jagged end lengths between shared and fetal-specific DNA molecules. (C) Relationship between JI-M deduced by methylation at CH sites in read2 and plasma DNA fragment sizes. (D) The cumulative JI-M between fetal-specific and shared DNA molecules. (E) The cumulative difference in JI-M, from 130 bp to 160 bp, between fetal and shared (mainly of maternal origin) DNA sequences. The black line represents the cumulative difference in jaggedness index between the shared (mainly of maternal origin) and fetal-specific DNA molecules pooled from all pregnant subjects. The positive values indicate relative higher jaggedness for molecules below a particular size cutoff. (F) The correlation between the average jagged end length within 130–160 bp and fetal DNA fraction. The JI-M represents the jagged index deduced from the methylated signals at CH sites.
