Table 2. Statistics of main effect quantitative trait loci detected in genome wide scan in the full data set.

MMU	Traits	Peak (cM)a	Flanking markersb				Estimate				%var
			Left	Right	F	LOD	a	s.ea	d	s.ed
1	ADG35–42**	22	rs3696088	rs13472794	15.83	6.766	−0.107	0.020	−0.027	0.026	3.11
1	ADG28–42**	23	rs3696088	rs13472794	25.91	10.968	−0.108	0.015	−0.027	0.021	4.99
1	ADG28–35**	24	rs3696088	rs13472794	10.63	4.568	−0.110	0.024	−0.027	0.032	2.11
2	ADG14–21**	71	rs3144393	rs13476878	26.27	11.115	0.061	0.009	0.028	0.012	5.05
2	ADG7–21**	79	rs3144393	rs13476878	15.18	6.491	0.024	0.006	0.035	0.009	2.98
2	BW28**	79	rs3144393	rs13476878	11.88	5.096	0.548	0.187	1.082	0.276	2.35
2	BW21**	81	rs3144393	rs13476878	14.21	6.083	0.427	0.118	0.708	0.179	2.80
2	ADG7–14	96	rs13476878	rs3143843	8.13	3.500	−0.018	0.006	0.024	0.009	1.62
2	BW14**	101	rs13476878	rs3143843	10.27	4.414	−0.032	0.064	0.400	0.089	2.04
2	BW7**	103	rs3143843	rs6335805	10.46	4.497	0.077	0.044	0.269	0.063	2.08
3	ADG28–35**	25	rs3663409	rs13477132	13.32	5.708	0.040	0.013	0.075	0.019	2.63
3	ADG28–42	30	rs3663409	rs13477132	10.55	4.534	0.027	0.009	0.045	0.013	2.09
3	ADG7–42**	58	rs3663873	rs13477430	12.94	5.546	0.027	0.006	0.026	0.009	2.55
3	BW42**	61	rs3663873	rs13477430	10.78	4.632	0.988	0.239	1.011	0.405	2.14
3	BW35	64	rs3663873	rs13477430	8.95	3.851	0.999	0.246	0.713	0.438	1.78
3	ADG21–28	120	rs3724562	CEL–3_159340478	8.85	3.811	0.057	0.014	−0.011	0.027	1.76
4	ADG7–21**	63	rs6324470	rs3659226	10.15	4.363	−0.023	0.006	0.015	0.008	2.02
4	BW21	64	rs6324470	rs3659226	7.95	3.426	−0.400	0.110	0.262	0.169	1.59
4	BW28**	64	rs6324470	rs3659226	10.64	4.572	−0.738	0.175	0.486	0.269	2.11
4	BW35	67	rs6324470	rs3659226	8.08	3.480	−0.733	0.212	0.667	0.342	1.61
5	ADG7–42	76	rs3720626	rs3706737	8.52	3.669	0.020	0.005	−0.007	0.007	1.70
5	ADG28–42	78	rs3720626	rs3706737	8.94	3.850	0.029	0.008	−0.020	0.012	1.78
6	ADG7–21	23	rs13478727	rs13478839	8.11	3.495	0.019	0.006	0.021	0.009	1.62
6	BW28**	27	rs13478727	rs13478839	14.07	6.026	0.885	0.177	0.544	0.268	2.77
6	BW35**	27	rs13478727	rs13478839	16.54	7.064	1.157	0.203	0.316	0.307	3.24
6	BW42**	28	rs13478727	rs13478839	15.88	6.789	1.124	0.203	0.428	0.304	3.12
6	ADG7–42**	29	rs13478727	rs13478839	16.40	7.009	0.030	0.005	0.010	0.008	3.22
6	ADG21–28**	30	rs13478727	rs13478839	16.65	7.112	0.076	0.013	0.026	0.019	3.26
10	ADG7–14**	32	CEL-10_58149652	rs13480647	10.82	4.647	−0.026	0.006	−0.020	0.010	2.14
10	ADG28–42	32	CEL-10_58149653	rs13480648	10.65	4.578	0.038	0.008	−0.007	0.013	2.11
10	ADG28–35	36	CEL-10_58149654	rs13480649	8.77	3.777	0.056	0.013	−0.010	0.021	1.75
10	BW42	37	CEL-10_58149655	rs13480650	9.08	3.907	0.864	0.207	−0.270	0.319	1.81
10	ADG21–28	44	rs3717445	rs13480707	8.39	3.611	0.053	0.013	−0.016	0.019	1.67
10	ADG7–42**	47	rs13480707	rs13480754	10.05	4.322	0.023	0.005	−0.008	0.008	2.00
11	ADG21–28**	26	rs6276300	rs6199956	17.78	7.584	0.073	0.014	0.053	0.022	3.48
11	ADG7–42**	28	rs6276300	rs6199956	20.51	8.726	0.034	0.006	0.012	0.009	3.99
11	BW42**	28	rs6276300	rs6199956	18.86	8.038	1.258	0.215	0.439	0.335	3.68
11	BW28**	29	rs6276300	rs6199956	13.66	5.851	0.873	0.187	0.563	0.291	2.69
11	BW35**	29	rs6276300	rs6199956	17.53	7.482	1.176	0.214	0.573	0.333	3.43
12	ADG7–14	61	rs6288403	rs6390948	8.91	3.836	−0.022	0.006	0.016	0.008	1.77
18	ADG7–42	8	rs13483233	rs3723947	8.53	3.673	0.021	0.005	0.002	0.007	1.70
18	BW35	8	rs13483233	rs3723947	9.15	3.938	0.819	0.192	0.042	0.272	1.82
18	BW42	8	rs13483233	rs3723947	8.61	3.707	0.802	0.193	0.043	0.275	1.71
18	ADG14–21	36	rs3670254	rs3718618	8.59	3.698	0.038	0.009	−0.001	0.014	1.71

Abbreviations: a, additive effect; d, dominance effect; MMU, mouse chromosome; s.e_a, standard error of additive effect; s.e_d, standard error of dominance effect; %var, percentage of phenotypic variance accounted for by quantitative trait loci.

^aPeak position of quantitative trait loci detected in Kosambi centimorgans.

^bFlanking markers (left and right) of the quantitative trait loci peak.

^**Quantitative trait loci with an F-value that exceeded the 1% genome-wide permutation threshold.

Other quantitative trait loci exceeded the 5% threshold.

A positive estimate indicates that the effect of the recurrent quantitative trait loci genotype is larger than the effect of the heterozygous genotype.