Allele-specific methylation. (A) Pedigree illustrating design of the mouse cross. Circles denote females and squares males. Black bars represent chromosomes derived from the C57BL/6J parents (B6) and white bars are chromosomes derived from the DBA/2J parents (DBA). (B) Allele-specific methylation sites between B6 and DBA female parents. The number of cytosines differentially methylated in each 100-kb bin is shown on the Y-axis and the genomic position of the bin is on the X-axis. All sites plotted are significant, and the horizontal dashed line represents the significance threshold for the 100-kb bin. (C) Hierarchical clustering of mice (columns) and allele-specific methylation sites (rows) for CG, CHG and CHH differentially methylated cytosines. Red indicates increased methylation and green indicates decreased methylation relative to other samples. f, female; m, male. (D) Allele-specific methylation sites identified using all eight mice. The number of C residues in each bin is on the Y-axis and the genomic position is on the X-axis. All sites plotted are significant, and the horizontal dashed line represents the significance threshold for each bin. (E) Methylation levels across all samples, showing allele-specific methylation of the gene Hspg2. The height of the bar represents percentage methylation from 0 to 100%. Gray represents missing data. The minus sign at the end of each sample denotes data from the minus strand.