Extended Data Table 2.

Summary of statistics from the genome structure calculation process for the eight cells analysed in the paper. The separate statistics for calculations involving 400 to 100 kb particles relate to the different stages of the hierarchical structure calculation protocol (see Supplementary Methods for details), with the last section representing the final, highest quality structures.

Cell	400 kb Particles				200 kb Particles				100 kb Particles (without ambiguous restraints)				100 kb Particles (with ambiguous restraints)
	RMSD*	NRest†	%V§ >3	%V§ >4	RMSD*	NRest†	%V§ >3	%V§ >4	RMSD*	NRest†	%V§ >3	%V§ >4	RMSD*	NRest†	%V§ >3	%V§ >4
1	0.13	26,453	2.94	0.76	2.32	43,150	1.29	0.08	0.56	71,729	2.81	0.57	0.41	74,945	2.29	0.22
2	0.29	22,838	0.16	0.00	0.50	35,244	0.29	0.00	0.88	47,598	1.04	0.15	0.63	56,159	0.74	0.13
3	0.24	17,944	0.81	0.28	0.51	21,049	1.66	0.08	0.89	22,822	4.82	1.36	0.70	25,952	2.87	0.42
4	0.33	25,126	2.35	0.68	0.58	37,594	1.26	0.14	1.03	50,516	2.49	0.94	0.74	60,420	1.14	0.17
5	0.32	23,062	1.18	0.30	0.65	34,103	0.86	0.10	1.08	44,298	2.12	0.73	0.86	51,824	1.24	0.21
6	0.38	25,084	0.60	0.10	0.69	35,526	0.70	0.06	1.09	44,687	0.99	0.22	0.91	53,710	0.74	0.17
7	0.81	18,301	0.07	0.04	1.26	26,585	0.03	0.00	1.91	33,588	0.11	0.01	1.75	39,257	0.13	0.02
8	0.49	15,877	0.00	0.00	0.93	22,956	0.00	0.00	1.52	28,083	0.02	0.02	1.26	32,482	0.03	0.02

^*The precision of structure ensembles in terms of mean pairwise all-particle RMSDs, in units of particle radii.

^†Restraint numbers include all experimental Hi-C contacts between non-adjacent particles, and thus increase as the particle size decreases. (NB – A single restraint may correspond to multiple Hi-C contacts, i.e. between the same two particle regions.)

^§The percentage of violated restraints was calculated for thresholds of 3.0 and 4.0 particle radii, respectively.