. 2006 Mar;172(3):1955–1965. doi: 10.1534/genetics.105.048686

TABLE 4.

Least-squares mean absolute difference (centimorgans), bias (centimorgans), and percentage of QTL position estimates at or flanking the QTL obtained from the IBD method using different haplotype sizes in six alternate scenarios with 1-cM marker spacing

		No. of markers used in IBD method
Alternate scenario		1	2	4	6	10
Noncentral QTL position	LSMD	1.53^a	1.33^b,c	1.19^d	1.23^c,d	1.38^b
Bias	0.62	0.60	0.53	0.52	0.51
69.5%	71.5%	71.1%	66.8%
Random founder allele frequencies	LSMD	1.57^a	1.36^b	1.32^b	1.33^b	1.36^b
Bias	0.016	0.003	−0.034	0.038	−0.025
63.9%	64.2%	64%	63.9%
“Worst-case” scenario	LSMD	2.67^a	2.61^a,b	2.38^c	2.38^c	2.45^b,c
Bias	1.75	1.91	1.60	1.55	1.56
35.0%	37.9%	37.2%	36.8%
Effective population size = 50	LSMD	1.91^a	1.66^b	1.53^c	1.64^b,c	1.68^b
Bias	−0.182	−0.034	−0.013	0.172	0.004
56.6%	60.0%	54.9%	56.7%
Effective population size = 200	LSMD	1.44^a	1.18^b	1.15^b	1.09^b	1.17^b
Bias	0.017	−0.009	−0.107	−0.029	−0.075
70.0%	71.8%	72.3%	70.9%
Smaller QTL effect	LSMD	1.83^a	1.76^a	1.55^b	1.60^b	1.80^a
Bias	−0.016	−0.083	−0.056	−0.086	−0.024
			51.6%	56.6%	54.8%	49.2%

The mean absolute difference of the QTL position estimate from its true position and bias for the IBD mapping method used in populations created under six alternate scenarios with 1-cM marker spacing are shown. The percentage of position estimates at or flanking the true QTL position is given for each haplotype size except for one marker. For a given alternate scenario, least-squares means with different superscripts (a, b, c, d) are significantly different (P < 0.05).