Fig. 1

Occurrence of probes from the set of 120 characterized by FDR q < 0.05. a. Pop-diff probes (M_av_diff >1). b. Weakly differentiating probes (M_av_diff <1). Vertical axis — count of probes targeting CpG sites divided into categories listed along the horizontal axis: SNP_1CpG or SNP_2CpG — differentiating SNP in the first or second position of the interrogated CpG as the only confounding factor; SNP_(1,2) CpG & other — SNP in the interrogated CpG combined with other confounding factors; Other — probes with the confounding factors other than SNP in the interrogated CpG (SNPs in the probe sequence outside the interrogated CpG, indels, multi-map, repeats, mixed etc.); Clean — probes with no confounding factor, potentially the only probes indicating true methylation level differences