Table 2. Comparison of the PHASE.big, PHASE.small and SNPHAP programs using phase known data sets.

Gene name		ApoE			LPL
Target region (kb)		5.5			9.7
No. of subjects		96			71
No. of SNPs		22			69
No. of heterozygous genotypes		283			1154
Average no. of heterozygous genotypes per subject		3			16
Nucleotide diversitya		0.0005 ± 0.0003			0.002 ± 0.001
Algorithm		PHASE.big	PHASE.small	SNPHAP	PHASE.big	PHASE.small	SNPHAP
Run time	Pre-filterb	2 h	6 h	1 min	3 h	9 days	90 s
	Post-filterc	2 h	6 h	1 min	3 h	7 days	1 min
Accuracy of full haplotyped	Pre-filter	74 (77%)	74 (77%)	79 (82%)	37 (52%)	38 (53%)	30 (42%)
	Post-filter	73 (76%)	73 (76%)	77 (80%)	32 (45%)	38 (53%)	27 (39%)
Accuracy of heterozygous genotypese	Pre-filter	253 (91%)	253 (91%)	258 (93%)	1051 (91%)	1058 (92%)	1033 (89%)
	Post-filter	252 (91%)	252 (91%)	256 (92%)	1035 (90%)	1053 (91%)	1022 (88%)

^aNucleotide diversity data is obtained from previous publications (17,18).

^bPre-filter, haplotypes predicted after excluding SNPs with no experimentally determined haplotype phase.

^cPost-filter, all SNPs were included in haplotype prediction, but SNPs with no experimentally determined haplotype phase were excluded in the comparison analysis.

^dThe number of subjects (or percentage of donors) whose complete haplotypes are correctly constructed.

^eThe number of heterozygous genotypes (or percentage of heterozygous genotypes) with correct haplotype phase assignment.