Allele-specific chromatin accessibility in early adolescence mouse liver resolved on a Collaborative Cross graph pangenome

Reads were mapped to the Collaborative Cross pangenome graph and phased into CC032 and CC072 alleles. Because no peak caller currently works directly on minigraph-cactus graphs, reads were surjected to GRCm38 for peak calling with MACS2.

Counting phased reads on both alleles at 102,412 reproducible cCREs and testing for differential accessibility identified 1,805 allele-specific cCREs (1.7%) between the maternal and paternal genomes. About 72% of these carry SNVs and/or SVs from one allele, and they are enriched in promoters, introns and intergenic regions as well as in SINE, LINE and LTR transposable-element subfamilies.