MOESM1 of Genetic and epigenetic variation among inbred mouse littermates: identification of inter-individual differentially methylated regions

Additional file 1: Table S1. Variant calls from whole genome sequencing of two Avy mice, one yellow and one pseudoagouti. The variant calls and associated genomic coordinates are relative to the NCBI37/mm9 genome assembly. Table S2. Validation of variant calls. A set of 105 SNP variants were selected at random from those that differed between the two mice or were heterozygous in both mice. Of the 96 that could be PCR amplified and sequenced, those that did or did not validate are shown. Table S3. Variably methylated regions designated iiDMRs. A list of 356 regions that display differential methylation between inbred individuals, generated from 6 adjacent CpGs that support differential methylation and a difference of at least 20Â % between the highest and lowest value. Values from the Yellow excluded from calling regions. Table S4. Variably methylated regions that overlap ERV elements, designated ERV iiDMRs. A list of 55 regions that display differential methylation between inbred individuals and overlap with ERV elements from the UCSC mm9 repeatmasker database. Differentially methylated regions were generated from 6 adjacent CpGs that support differential methylation and a difference of at least 20Â % between the highest and lowest value. Values from the Yellow mouse were excluded from calling regions. Table S5. Primers used in the study