To calculate the total number of C/CG/CHG/CHH theoretically captured, MSPI, whose restriction site is C-CGG with ‘-’ representing digestion position, were used to simulate the digestion process. The reference genome was firstly cut into fragments. Then we select the fragments with length ranges from 40 to 220 bp, based on which the number of C/CG/CHG/CHH captured theoretically was calculated separately.

Here, “C/CG/CHG/CHH covered” means C/CG/CHG/CHH which has the depth of covering reads higher than the threshold defined by the users.

Definition of putative mC/mCG/mCHG/mCHH : cytosine, which methylation ratio is greater than “lower bound of 95% confidence interval of methylation ratio” and equal or lower than “upper bound of 95% confidence interval of methylation ratio”.

We calculate the total number of mC/mCG/mCHG/mCHH from mc format file.

The covered depths of all the cytosines included in the following analysis are equal or greater than user defined number ( n value in DNA methylation analysis section ).

>> The distribution of functional elements in each methylation level grade. These four figures are relevant to five input parameters in "DNA methylation analysis", which including "P value", "Methylation scales" (l1, l2, l3, l4 value). "P value" determines the total number of functional elements, which were included in these four images. Elements, which fraction of captured region in the region of itself is greater than the threshold setted by users, were included in the above analysis. "Methylation scales" (l1, l2, l3, l4 value) determines the corresponding methylation level grade value. We categorizes cytosines into CG, CHG and CHH content to calculate the methylation level of each element, separately. And then calculate the total number of element in each methylation level grade to draw these four images. We can get these result data with mc format file and the chromosome coordinate file of functional element. These images show the difference of element quantity in different methylation level grade among different samples.

>> methylation level of CGI and flanking region

CGI

>> genome methyltion scan Definition of putative mC/mCG/mCHG/mCHH : cytosine, which methylation ratio is greater than “lower bound of 95% confidence interval of methylation ratio” and equal or less than “upper bound of 95% confidence interval of methylation ratio”. In this section, we mainly compared the difference of methylation state among these samples from the following aspects: (1) The methylation level in different cytosine content. (2) The total number of theoretical, covered, captured and methylated cytosine. (3) Total number of captured and methylated cytosine in each cytosine content. (4) Total number of methylated cytosine in each methylation level grade with each cytosine content.

>>Methylation level of each genomic element or gene region in different methylation patterns (C/CG/CHG/CHH).