Congruence as a measurement of extended haplotype structure across the genome

Table 3 Numeric comparison of ExHap, GERMLINE, and Sweep.

			ExHap	GERMLINE	Sweep
	Range in base pairs	Cohort	Percent Congruet	Avg # of Shared Segments per chromosome, 0.75 Mb min length	Avg EHH of 30 Core Haplotypes with Highest EHH at 600 Kb From Core
Chr2	135460477-136506753	CEU	79.0	19.1	0.69
		YRI	7.0	2.8	0.59
Chr8	99920891-100880665	CEU	72.7	9.3	0.90
		YRI	70.0	7.9	0.84
Chr10	103101047-104210566	CEU	9.1	4.5	0.51
		YRI	44.5	3.0	0.70

Three regions were selected based on patterns of congruence in HapMap CEU and YRI cohorts. Allele identity plots of the regions are presented in Figures 5, 6, and 7. GERMLINE results are expressed as average number of shared segments per chromosome to account for the difference in the number of chromosomes between CEU (n = 176) and YRI (n = 200)

ISSN: 1479-5876