Methylation status of CCWGG sites and bisulfite conversion efficiency in bis-sol and bis-gel.

Fully CCmWGG and partially methylated CYWGG sites were discovered by comparing the sequencing reads against the +/− bisulfite converted reference. Methylated Cs will show up as a SNP conversion T → C (bisulfite converted reference → sequence read) within the CCWGG motif. A T → C SNP outside this motif indicates an incomplete bisulfite conversion (unconverted C). Comparing this number with the total number of Cs present in the DH10B genome, indicates the bisulfite conversion efficiency of the library protocol.