Fig. 2

Allele-specific analysis. a Allele-specific analysis of the GM12878 cell line. Phasing data were gathered from the Illumina Platinum Genomes Project. In total, 2,239,492 high quality SNPs from GM12878 data were used to distinguish both alleles. Around 6 % of the read pairs were assigned to each parental allele and used to build the allele-specific contact maps. b Intra-chromosomal contact maps of inactive and active X chromosome of the GM12878 cell line at 500-kb resolution. The inactive copy of chromosome X is partitioned into two mega-domains which are not seen in the active X chromosome. The boundary between the two mega-domains lies near the DXZ4 micro-satellite