Table 7:

Sign Test Comparisons of LD Measures in Phased and Unphased Haplotypes

Ethnicity/Country		D’	Wn	WLoc1/Loc2	WLoc2/Loc1	N_Haplotypes
African American 2N = 144	unphased > phased	44	42	45	46	12
	unphased = phased	5	4	4	4	7
	locus pairs	55	55	55	55	55
	p-values	8.70E-06	0.000114	2.06E-06	4.34E-07	3.31E-05
European American 2N = 424	unphased > phased	48	45	49	47	15
	unphased = phased	2	2	2	2	5
	locus pairs	55	55	55	55	55
	p-values	1.31E-08	2.06E-06	1.82E-09	8.07E-08	0.001016
Asian American 2N = 230	unphased > phased	42	42	43	44	17
	unphased = phased	2	2	2	2	8
	locus pairs	55	55	55	55	55
	p-values	0.000114	0.000114	3.31E-05	8.70E-06	0.006456
Hispanic 2N = 232	unphased > phased	43	45	45	43	16
	unphased = phased	1	1	2	2	6
	locus pairs	55	55	55	55	55
	p-values	3.31E-05	2.06E-06	2.06E-06	3.31E-05	0.002667
ARGENTINA 2N = 348	unphased > phased	43	49	46	46	18
	unphased = phased	0	0	0	0	2
	locus pairs	55	55	55	55	55
	p-values	3.31E-05	1.82E-09	4.34E-07	4.34E-07	0.014454
AUSTRIA 2N = 40	unphased > phased	34	42	37	39	20
	unphased = phased	7	6	10	10	16
	locus pairs	55	55	55	55	55
	p-values	0.104789	0.000114	0.014454	0.002667	0.058064
CHINA 2N = 932	unphased > phased	15	14	15	15	1
	unphased = phased	0	0	0	0	1
	locus pairs	15	15	15	15	15
	p-values	6.10E-05	0.000977	6.10E-05	6.10E-05	0.000977
CZECH REPUBLIC 2N = 336	unphased > phased	48	51	48	49	16
	unphased = phased	1	1	2	2	7
	locus pairs	55	55	55	55	55
	p-values	1.31E-08	2.05E-11	1.31E-08	1.82E-09	0.002667
EGYPT 2N = 56	unphased > phased	35	33	33	33	21
	unphased = phased	10	9	10	9	13
	locus pairs	55	55	55	55	55
	p-values	0.058064	0.177001	0.177001	0.177001	0.104789
GERMANY 2N = 276	unphased > phased	47	49	48	48	11
	unphased = phased	4	3	4	4	8
	locus pairs	55	55	55	55	55
	p-values	8.07E-08	1.82E-09	1.31E-08	1.31E-08	8.70E-06
GREECE 2N = 100	unphased > phased	41	44	42	42	16
	unphased = phased	7	7	7	7	15
	locus pairs	55	55	55	55	55
	p-values	0.000355	8.70E-06	0.000114	0.000114	0.002667
ITALY 2N = 268	unphased > phased	21	21	21	21	0
	unphased = phased	0	0	0	0	0
	locus pairs	21	21	21	21	21
	p-values	9.54E-07	9.54E-07	9.54E-07	9.54E-07	9.54E-07
KUWAIT 2N = 116	unphased > phased	41	44	42	44	13
	unphased = phased	5	5	6	6	11
	locus pairs	55	55	55	55	55
	p-values	0.000355	8.70E-06	0.000114	8.70E-06	0.000114
SWITZERLAND 2N = 44	unphased > phased	36	33	38	36	19
	unphased = phased	9	9	10	10	18
	locus pairs	55	55	55	55	55
	p-values	0.030029	0.177001	0.006456	0.030029	0.030029

The “locus pairs” rows show the total number of locus pairs built for the ethnic group or country. The “unphased > phased” rows indicate the number of locus pair where value of each category shown at the top for unphased haplotypes is larger than that for phased. The “unphased = phased” rows indicate the number of locus pairs where the value of each category for both unphased and phased haplotypes are equal. For example, 44 in the “unphased > phased” row and D’ column means that 44 of 55 locus pairs had higher D’ value for unphased haplotypes; 5 in the “unphased = phased” row and D’ column indicates that 5 of 55 locus pairs had equal value. Sign tests were performed, and p-values are shown for each category. The uncorrected threshold of significance for these p-values is 0.05. Correcting for 14 comparisons in each category [32], the threshold of significance is 3.57E-03; p-values below this threshold are underlined. Correcting for all 70 comparisons in the table, the threshold of significance is 7.14E-04; p-values below this threshold are shown in bold.