Table 3.

Markers significant in the GBS indica panel

Marker	QTL	Chr	Position	Posterior probability	p-value	q- value	Number obs. minor allele
S01_25684060	qi01–1	1	25 684 060	0.42	1.69E-03		46
S01_25685951		1	25 685 951	0.41	1.73E-03		45
S03_16707839	qi03–1	3	16 707 839	0.17	7.12E-05	0.14	72
S03_16748994		3	16 748 994	0.61	3.33E-06	0.03	74
S03_16777244		3	16 777 244	0.87	3.73E-06	0.02	61
S03_16789846		3	16 789 846	0.66	1.90E-05	0.08	59
S06_10959696	qi06–1	6	10 959 696	0.75	6.81E-05	0.16	7
S07_18744029	qi07–1	7	18 744 029	0.45	6.49E-04		24
S07_18908531	qi07–2	7	18 908 531	0.53	9.17E-04		17
S08_24524064	qi08–1	8	24 524 064	0.54	3.25E-05	0.11	38
S08_24620154	qi08–2	8	24 620 154	0.51	1.02E-04		36
S09_12474280	qi09–1	9	12 474 280	0.83	5.65E-07	0.01	33
S09_12772588	qi09–2	9	12 772 588	0.10	5.85E-05	0.16	30
S11_28821256	qi11–1	11	28 821 256	0.59	1.06E-03		14

In bold, markers significant in the initial analysis; in italics, initial probability of the markers being significant through sub-sampling