Table 1.

Assignment of paired-end reads to chimeric fragments. To each of the four possible relative orientations of mapped paired-end reads, we assigned a chimeric fragment class that results from which ends of a given pair of restriction fragments re-ligate with each other

Paired-end orientation		Chimeric fragment class
Inwards		3′–5′ re-ligation	‘0’
Outwards		5′–3′ re-ligation	‘1’
Both forward		3′–3′ re-ligation	‘2’
Both reverse		5′–5′ re-ligation	‘3’