Characteristics of Arabidopsis methylome generated by the combined MspJI-seq data. (A) The density of 5 mCs and repetitive sequences throughout five chromosomes of Arabidopsis genome. The density of 5 mCs and MspJI-seq tags were calculated as their numbers in 100 kb intervals, and the density of repeats were calculated as repetitive sequence’s length in 100 kb intervals. (B-E) The relative methylation levels of genic regions and high-CpG regions (indicated by CGNR\CHGR\CHHR contexts). Each genic or high-CpG region were equally divided into 20 intervals and their 1 kb surrounding sequences were divided into 100 bp intervals. The figures display average methylation levels on intervals of gene bodies (B), exons and introns (C), CGIs (D) and the CGIs overlapping with gene promoters (E). (F) The normalized methylation levels of housekeeping genes and hypervariable genes. The calculation of relative methylation levels of gene sequences is just as that of intervals.