a) Methylation status of c9orf72 region in BAC data for repeats < 200 (WT), 200-750 (Cluster1,orange) and > 750 (Cluster2,red) and control (Hues64, WGBS) b) Single read methylation on a sample of 500 BAC minus strand reads sorted by repeat count (row split 200 and 750 repeats, n=423,63,14). c) Difference in mean CGI methylation of intron and promoter per read on minus strand. Reads binned by detected repeat length for BAC (n=2066 WT; 315 Cluster1; 72 Cluster2) and patient 24/5#2 (n=925 WT; 362 Cluster1; 153 Cluster2). Two sided Wilcoxon rank sum test, corrected for multiple testing (Holm), q-vals: * 0.05 - 0.01; ** 0.01 - 0.001; *** < 0.001. Median methylation differences between promoter CGI [95%CI] for WT -2.3e-5 [CI: -5.6e-6:-1.5e-5, q=7.4e-3] and Cluster1 -0.01 [CI: -7.1e-5:-3.4e-2, q=1.4e-17] and Cluster2 -0.46 [CI: -0.58:-0.37, q=1.0e-26].