Extended data for manuscript "Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes"

Resolving the three-dimensional structure of chromatin with haplotype specificity remains a fundamental challenge for understanding genetic and epigenetic contributions to gene regulation in healthy development and in disease. Phasing of chromatin contacts derived by ligation-dependent methods relies on high single-nucleotide variant (SNV) density, which limits its applicability in human genomes where SNVs are sparse. Here, we present CoPhasing, a strategy that leverages the intrinsic haplotype fidelity of Genome Architecture Mapping (GAM), a ligation-free method that inherently captures haplotype-matched genomic neighborhoods in thin nuclear slices. CoPhasing assigns SNV-free reads to their haplotype through proximity to informative reads, enabling efficient and accurate phasing even in SNV-sparse regions. Applying CoPhasing genome-wide reveals extensive,previously inaccessible structural heterogeneity between human homologous chromosomes, demonstrating the power of this approach to investigate allele-specific differences in 3D genome organization and their relevance to gene regulation and disease.This repository provides high-resolution cophased and nonphased segregation tables for the full set of SNPs F123 mESC GAM dataset and the results of the final permutation test results (differential contacts) for H1 hESC GAM dataset.