Table 2.

Configurations of unbalanced interactions. Examples of unbalanced read pair counts for each configuration. According to our assignment of relative paired-end read orientations to chimeric fragment classes, the configurations differ in how many chimeric fragment classes are predominantly observed and how many restriction fragment ends are involved in re-ligations (see also Supplementary Figure S3). We assigned a label and color to each configuration

Example	Class	Ends involved	Label	Color
100:10:10:10	1	2	0X	–
10:100:10:10	1	2	1X	–
10:10:100:10	1	2	2X	–
10:10:10:100	1	2	3X	–
50:15:50:15	2	3	02	Red
50:15:15:50	2	3	03	Green
15:50:50:15	2	3	12	Magenta
15:50:15:50	2	3	13	Blue
50:50:15:15	2	4	02	Pink
15:15:50:50	2	4	23	Turquoise