Fig. 1

Different CpG methylation levels obtained from identical PBAT libraries using different HCS and RTA versions. a CpG methylation levels determined by single-end PBAT-seq. CpG methylation levels in 100 kb windows are shown as a box plot (left). Different proportions of G among the four bases in R1 obtained using different HCS and RTA versions are shown as a line plot (right). b Correlation between the CpG methylation levels determined using HCS v2.0.5, v2.0.10, and v2.0.12. CpG methylation values of 100-kb non-overlapping sliding windows across the autosomes are plotted with a linear regression line (red). c Differences between the CpG methylation levels determined using HCS v2.0.5 and v2.0.12 against the CpG density. CpG methylation values were calculated in 100-kb non-overlapping sliding windows across the autosomes. All 100 kb windows were grouped into nine classes according to the number of contained CpG. d CpG methylation levels determined by paired-end PBAT-seq (IMR-90). CpG methylation levels in 100 kb windows are shown as a box plot (left). Different proportions of G in R1 and C in R2 obtained using different HCS and RTA versions are shown as a line plot (right)