Utility of Infinium BeadChips on vertebrate genomes. (A) SeSAMe workflow of species and strain inference and genome-specific preprocessing. (B) Annotation of four Infinium BeadChip probes on the number of functional probes across 310 genomes (showing 33 representative species). (C) Genic view of probe retention of three generations of Infinium BeadChips. (D) Evolutionarily conserved versus non-conserved regions in the cross-species retention rate of probes on the MM285 array. (E) A schematic illustration of six groups of SNP influences on DNA methylation reading (R = A,G; Y=C,T,U; D = A,G,T). (F) Validation of strain-specific SNP influence on DNA methylation readings in 191 inbred mouse strain samples. Three wild-derived strains (CAST_EiJ,PWK_PhJ and MOLF_EiJ) were shown separately due to their higher SNP number.