Fig. 5

Human Mandinka samples display rDNA epivariation. A Analysis of human Mandinka LCL WGBS samples shows allele-specific methylation levels (FDR < 0.01) at positions -413 and 7980 of the KY962518.1 rDNA reference. B Average methylation levels around -413 and 7980 are correlated with rDNA copy number estimated from WGS. C Allele-specific methylation affects rRNA expression. Methylation levels around position 7980 are inversely correlated with allele-specific frequency in rRNA-seq (left panel), and correlation between DNA (WGS) and rRNA allele frequencies improves when accounting for methylation at position 7980 (right panel). D Analysis of ultra-long-read Nanopore data from human sample HG02723 suggests that both allele at position 7980 (shape) and average methylation level across the rDNA coding unit (fill color) tend to be consistent along single molecules, with some exceptions. Each row represents an individual read; gaps separate units that were reported on split alignments