DNA reads were aligned against GRCH37 using Bismark58 software version 0.14.3, permitting at most one mismatch, considering both sequence and bisulfite conversion mismatches. Methylation calls for each CpG were extracted using Bismark methylation extractor tool. Read alignment revealed that many reads could be mapped to both AREG and the AREG pseudogene due to high degree of homology. To allow mapping of AREG, the AREG pseudogene was masked during analysis, and vice-versa. Differential methylation analysis comparing Panc1-3D7 and Panc1-2G6 was performed using Bioconductor DSS software version 2.10.059. Differentially methylated loci (DML) were determined by >0.99 posterior probability of the difference in mean methylation levels being >0.3. Differentially methylated regions (DMR) were also detected by joining DMLs with p-value less than 0.01. DMRs have a minimum length >50 bps, minimum number of DML >3 and >50% of CpG sites with p-value < 0.01. DMRs with distance less than 100 bps were merged. DMLs and DMRs were annotated using methylKit60 version 0.9.5, where we defined the promoters as +/− 1000 bp from TSS and CpG shores +/− 2000 bp flanking each side of the CpG island.