Table 4.

Block similarity among several methods of haplotype block partitioning.

	HOT	MB	HB	MDL	GAM	GAB	GPG	GPF
HOT	1.00	0.32	0.31	0.16	0.13	0.26	0.39	0.40
MB	0.32	1.00	0.65	0.36	0.30	0.58	0.60	0.56
HB	0.31	0.65	1.00	0.41	0.35	0.60	0.56	0.54
MDL	0.16	0.36	0.41	1.00	0.54	0.42	0.30	0.29
GAM	0.13	0.30	0.35	0.54	1.00	0.41	0.25	0.24
GAB	0.26	0.58	0.60	0.42	0.41	1.00	0.57	0.55
GPG	0.39	0.60	0.56	0.30	0.25	0.57	1.00	0.88
GPF	0.40	0.56	0.54	0.29	0.24	0.55	0.88	1.00

The similarity measure indicates the proportion of SNP pairs commonly shared by different partitionings on ten ENCODE regions. See Table 1 for method abbreviations.