Table 3.

Maximum linkage LOD scores and empirical genomewide (GW) p-values at 49.1 cM on chromosome 1 for LTR using different parameter specifications in MERLIN-REGRESS

Mean	LOD	GW P value*	Variance	LOD	GW P value*	Heritability	LOD	GW P value*
						0.1	5.05	0.01
3.01	7.47	0.03	0.0067	8.75	0.14	0.3	7.11	<0.01
3.06	8.01	<0.01	0.01	8.78	0.09	0.45	8.41	<0.01
3.12**	8.74	<0.01	0.02	8.74	<0.01	0.6	8.74	<0.01
3.19	8.29	<0.01	0.04	8.2	<0.01	0.75	7.12	0.08
3.29	3.59	<0.01	0.06	7.42	<0.01	0.9	4.36	0.19
						1	2.66	0.12

Parameter values for the mean, variance and heritability were, respectively, 3.12, 0.02 and 0.6, when not otherwise indicated

^*Empirical genomewide p-values for each statistical model were calculated using gene-dropping simulations implemented in the simulate option of MERLIN-REGRESS. P-values were based on 100 replicates of 371 randomly generated markers

^**The “presumed correct” model (bold) assumed a population mean for LTR of 3.12, a variance of 0.02 and a heritability of 0.6. Values of 3.01, 3.06, 3.12, 3.19 and 3.29 for mean LTR correspond to refractions of 0, −1, −2.5, −4 and −6.5 D, respectively, on the non-transformed scale