Parameter searching

We provided the default parameter search intervals for each of the four parameters of GMAP algorithm in Supplemental Table 3 
IMR90 10kb KR normalization (3) [GSE63525] GM12878 10kb KR normalization (3) [GSE63525] NHEK 10kb KR normalization (3) [GSE63525] K562 10kb KR normalization (3) [GSE63525] HMEC 10kb KR normalization (3) [GSE63525] HUVEC 10kb KR normalization (3) [GSE63525] MCF-7 40kb ICE (4) [GSE66733] MCF-10A 40kb ICE (4) [GSE66733] LNCaP 40kb ICE (4) [GSE73785] PC3 40kb ICE (4) [GSE73785] PrEC 40kb ICE (4) [GSE73785] ESC 40kb ICE (4) [GSE59027] NPC 40kb ICE (4) [GSE59027] Neuron 40kb ICE (4) [GSE59027]
Resolution represents the size of the genomic bin used for summing up Hi-C contact counts in the bin. 
Supplementary Table 2. Source of ChIP-Seq data used in this study. 

Factor Cell line [accession number] Notes

CTCF IMR90 [GSM935404], K562 [GSM733719], GM12878 [GSM733752], HMEC [GSM733724], NHEK [GSM733636], HUVEC [GSM733716]
The ChIP-Seq peaks can be found in the published work corresponding to the above provided accession number. 



  




  




  




  


Table 1 . Source of Hi-C data used in this study.

 1 
	. The optimized default

Supplementary Methods


Fitting of Gaussian mixture models using Expectation-Maximization algorithm

We used the popular R package 'mclust' to implement the Expectation-Maximization (EM) algorithm. Within mclust, EM algorithm is initialized using the partitions obtained from model-based hierarchical agglomerative clustering (MBHAC). Although there is no guarantee that the EM initialized by MBHAC will converge to the global optimum, it often provides reasonable starting points Here simple somatic mutations include point mutations, small insertions and deletions. 

Supplementary