Table 2.

Mapping statistics for different experimental replicates

Technology	HiSeq 100X2	HiSeq 100X2	HiSeq 100X2	HiSeq 100X2
Sample	N2 L1 Fed AvaII	N2 L1 Fed DpnII	N2 L1 Starved AvaII	N2 L1 Starved DpnII
GEO accession	GSM2041035- SRR3105470	GSM2041036- SRR3105472	GSM2041033- SRR3105465	GSM2041034- SRR3105468
Total number of reads	45,346,483	50,098,648	12,074,391	31,699,338
Both sides aligned	29,802,885	29,416,663	8,325,030	22,664,227
Concordant Pairs	20,376,818	16,485,927	4,352,019	12,630,225
intra-chromosomal Pairs	3,943,229	5,728,073	2,103,366	6,332,935
inter-chromosomal Pairs	1,712,801	3,814,807	559,830	2,321,074
Hi-C valid pairs	5,656,030	9,542,880	2,663,196	8,654,009
% Hi-C valid pairs	19	32.4	32	38.2