A multi-tissue regulatory atlas reveals adaptive noncoding variation in cattle

All_Samples.fwp.filter.non_overlapping.final.bed: Genomic coordinates of 499,326 nonredundant, non-overlapping, fixed-width CREs identified from 208 high-quality ATAC-seq samples. 74.biallelic.maf0.01.vcf.gz: A VCF file containing biallelic structural variants identified from long-read sequencing data of 74 cattle and retained after filtering for a minor allele frequency greater than 0.01. Digest_Bos_MboI.baitmap: A CHiCAGO-compatible bait map containing the genomic coordinates and identifiers of MboI restriction fragments selected as promoter-capture Hi-C baits. Digest_Bos_MboI.rmap: A CHiCAGO-compatible restriction map containing the genomic coordinates and identifiers of all MboI restriction fragments in the bovine reference genome. merged.208.coverage.txt: A raw CRE count matrix generated using the multicov function in BEDTools, containing read counts for 499,326 nonredundant CREs across the 208 ATAC-seq samples. merged.208.coverage.quantile.txt: Normalized CRE count matrix.