Fig. 4

Improved accuracy of ATAC-seq alignment to the CD-1 genome. A Venn diagram showing the number of ATAC-seq peaks called in both mm10 and CD-1, just in CD-1, and just in mm10. Reproducible peaks (see Methods) were called separately in the BPA Adopose, Control Adipose, BPA Sperm, and Control Sperm samples, and then combined into a single pan-sample peak set for CD-1 and one for mm10. B Barplots comparing the percentage of the indicated ATAC-seq peak sets overlapping with uniform SNPs and indels (left column), and with non-uniform SNPs (right column). CD-1 Unique: peaks that are called when mapping to CD-1 but not when mapping to mm10; mm10 Unique: peaks that are called when mapping to mm10 but not when mapping to CD-1; Common: peaks that are called both when mapping to CD-1 and to mm10. C Genome browser view of a control (Ctrl) adipose ATAC-seq peak called when mapping to CD-1 but not mm10. D Genome browser view of a control (Ctrl) adipose ATAC-seq peak called when mapping to mm10 but not CD-1. In both C and D, RPM-normalized ATAC-seq coverage is displayed, and the region of interest is highlighted; the genome to which reads were mapped is indicated at the top left of each browser view. P-values in this figure are exactly as described in Fig. 1