Fig. 3

Improved mappability and accuracy of WGBS alignments to the CD-1 genome. A Left panel: Barplots showing the number of non-duplicate reads mapped to either CD-1 or mm10 in the indicated samples (Sp. = sperm; Fat = adipose). Right panel: Barplots showing the difference between the number of nonduplicate reads mapped in CD-1 and mm10. Positive values indicate more reads mapped in CD-1 than mm10. B Histograms of reads mapping with mapping quality (mapQ) < 40 when mapping to CD-1 and to mm10. C Venn diagram showing the number of DMRs called in both mm10 and CD-1, just in CD-1, and just in mm10. All DMRs called in BPA vs. control in all samples examined in this study were combined into a single set of DMRs called after mapping to CD-1, and a single set called after mapping to mm10. D Barplots comparing the percentage of the indicated DMR sets overlapping with a uniform SNP or indel in which a C or G is in mm10 but not CD-1 (left column), or comparing the indicate DMR sets overlapping with a uniform SNP or indel in which a C or G is present in CD-1 but not mm10 (right column). CD-1 Unique: DMRs that are called when mapping to CD-1 but not when mapping to mm10; mm10 Unique: DMRs that are called when mapping to mm10 but not when mapping to CD-1; Common: DMRs that are called both when mapping to CD-1 and to mm10. E Barplots comparing the percentage of the indicated DMR sets overlapping with a non-uniform SNP of one of the indicated types. C <—> T: Some CD-1 mice have C and others T at the SNP; G <—> A: Some CD-1 mice have G and others A at the SNP. F, G Genome Browser views of adipose WGBS, showing methylation % and WGBS read coverage at DMRs called uniquely in CD-1 and mm10, as indicated. Ctrl = Control. P-values for this figure are exactly as described in Fig. 1