Characterisation of SNP haplotype structure in chemokine and chemokine receptor genes using CEPH pedigrees and statistical estimation

Table 2 Results from a comparison of pedigree-derived and estimated haplotype frequencies (n = 103).

Haplotype number	Haplotype	GP count	Pedigree frequency	MLOCUS frequency	Similarity index	MSE
1	11111111111111	60	0.2913	0.2936	0.0024	0.00001
2	11111112221111	39	0.1893	0.1909	0.0015	0.00000
3	11112122221111	35	0.1699	0.1719	0.0020	0.00000
5	11211211111111	21	0.1019	0.1001	0.0019	0.00000
4	21111121211121	20	0.0971	0.0882	0.0089	0.00008
6	11111111111211	18	0.0874	0.0919	0.0045	0.00002
8	11111111112111	5	0.0243	0.0223	0.0020	0.00000
7	11112121111111	4	0.0194	0.0186	0.0008	0.00000
	11112121211121	2	0.0097	0.0098	0.0001	0.00000
	11212122221111	1	0.0049	0.0049	0.0000	0.00000
	11111121211111	1	0.0049	0.0049	0.0000	0.00000
	11211211211111	0	0.0000	0.0022	0.0022	0.00000
		206	1.0000	0.9993	0.9869	0.00001

The total similarity index (I_F) and mean squared error (MSE) values are indicated at the bottom of the table. Haplotypes that are only present in MLOCUS estimates are denoted in italics. The haplotype number indicates the equivalent haplotype to those seven SNP haplotypes discussed in Clarket et al. 2001 [25].

ISSN: 1479-7364