Fig. 2

Coverage of CpGs across the genome. All samples visualized here were downsampled to 20× mean coverage per CpG. a Empirical cumulative distribution functions for median coverage, averaged across samples for HG002-HG007. b Standard deviation between replicate beta values for HG002 as a function of average coverage. The expected curve (computed based on the assumption that replicate beta values are independent and identically distributed estimates of a common proportion p) is added as a solid black curve. c Intersection of CpG coverage (min 5×) across Chromosome 1. Exact values of CpGs covered per assay are shown on the right. d Count and genomic annotation for CpGs uniquely covered by an assay (left) and uniquely not covered by an assay (right). Up5kb = 5 kb upstream distance from promoter region; Promoter = within 1 kb upstream of transcript start site. e Distribution of coverage in CpG shelves, shores, and islands. EM = EMSeq; MS = MethylSeq; SP=SPLAT; TS = TruSeq; TM = TrueMethyl. f Mean coverage curves around transcript start sites (TSS)