Table 4.

Statistics of QTLs from cofactor analysis

Year	Naive QTL(s) as cofactor(s): chr. (position)a	LOD scores of QTLs by cofactor analysis (chr. and position)b	R2 of QTLs by cofactor analysisc	New QTLs identified by cofactor analysis: chr. (position)d
2013	3 (56)	5.7 (9-40) Fig. S1	0.051	No
2013	9 (48)	7.8 (3-56) Fig. S2	0.07	No
2013	3 (56) + 9 (48)	N.S. Fig. S3	N.S.	No
2014	2 (21)	9.3 (5-24); 5.5 (5-78) Fig. S4	0.083; 0.050	5 (78)
2014	5 (25)	6.2 (2-23) Fig. S5	0.056	No
2014	2 (21) + 5 (25)	N.S. Fig. S6	N.S.	No
BLUEs 2012–2014	2 (30)	5.4 (1-67); 9.1 (3-69); 6.3 (9-40) Fig. S7	0.049; 0.081; 0.056	1 (67)
	3 (69)	6.8 (2-30); 5.7 (9-40) Fig. S8	0.062; 0.052	No
	9 (48)	6.2 (2-30); 7.4 (3-69) Fig. S9	0.056; 0.067	No
	2 (30) + 3 (69)	6.1 (9-40) Fig. S10	0.059	No
	2 (30) + 9 (48)	8.2 (3-69); 5.9 (5-83) Fig. S11	0.074; 0.053	5 (83)
	3 (69) + 9 (48)	6.7 (2-28) Fig. S12	0.06	No
	2 (30) + 3 (69) + 9 (48)	N.S. Fig. 6	N.S.	No

Chr., chromosome; Position, QTL peak position in centiMorgan (cM); LOD, logarithm of the odds; BLUEs, best linear unbiased estimates; N.S., non-significant

^aQTL(s) identified by naive QTL analysis (Table 3)

^bQTL(s) identified by cofactor QTL analysis after one or more QTL(s) identified by naive QTL analysis were used as cofactors

^cVariance explained (R²) of QTL(s) identified by cofactor QTL analysis

^dNew QTLs identified by cofactor QTL analysis that were not identified by naive QTL analysis