Fig. 4

a A comparison of the coverage of peak called regions in the reference and the Hap1 DPG. The smear represents ref-only peaks with no coverage in Hap1. b Identification of peak called regions that have a significant difference in coverage. c Summary of the overlap between altered peaks, confident peaks, repeats, and segmental duplications [58]. d The repeats that overlap altered peaks are enriched in Alu elements relative to their frequency in the RepeatMasker. The categories are chosen by grouping repeats by name prefix, summing their frequencies per group, and taking the largest groups. Remaining groups are labeled as “other.” The control regions are random genomic intervals with a width distribution identical to altered peaks