Impact of prior specifications in a shrinkage-inducing Bayesian model for quantitative trait mapping and genomic prediction

Table 2 The 20 markers with the strongest signals of association across chains in the analysis of the QTLMAS XII data

Marker			Closest true major QTL^(a)			2ln(BFm)			\|β_Q\|	E_post(β_m)			% PVEQ	E post( % PVE m)
Chr	Pos	MAF	MAF	Name	Dist	avg	min	max		avg	min	max		avg	min	max
1	19.5	0.28	0.28	M1	0.50	30	28	32	0.62	0.60	0.59	0.61	3.5	3.4	3.2	3.5
1	40.1	0.09	0.07	M2	-0.10	15	9	21	0.56	-0.35	-0.46	-0.17	0.9	0.6	0.3	0.8
1	77.7	0.28	0.29	M3	-0.47	28	22	32	0.37	0.43	0.41	0.46	1.3	1.7	1.6	1.9
2	26.9	0.44	0.44	M4	0.51	12	10	15	0.35	0.22	0.15	0.28	1.4	0.9	0.5	1.3
2	28.2	0.24	0.44	M4	-0.79	12	7	18	0.35	0.20	0.09	0.33	1.4	0.6	0.3	1.2
2	48.2	0.38	0.40	M6	0.42	25	14	32	0.37	-0.41	-0.45	-0.36	1.5	1.8	1.5	2.2
2	72.9	0.11	0.18	M7	2.01	11	8	15	0.50	0.15	0.04	0.24	1.6	0.2	0.1	0.4
3	13.2	0.33	0.40	M8	1.71	11	7	18	0.30	0.14	0.03	0.28	1.0	0.4	0.1	0.9
3	14.8	0.39	0.40	M8	0.11	8	6	12	0.30	-0.04	-0.08	-0.01	1.0	0.1	0.0	0.3
3	54.1	0.27	0.07	M9	5.90	11	6	16	0.68	0.12	0.01	0.21	1.3	0.3	0.0	0.5
3	60.1	0.16	0.07	M9	-0.10	24	20	29	0.68	-0.39	-0.41	-0.37	1.3	1.0	0.9	1.1
4	75.7	0.05	0.41	M12	0.36	26	12	32	0.58	-0.72	-0.78	-0.58	3.7	1.1	0.9	1.3
4	76.4	0.46	0.41	M12	-0.34	30	28	32	0.58	0.64	0.61	0.67	3.7	4.6	4.2	5.1
4	85.9	0.18	0.41	M12	-9.84	10	9	12	0.58	0.12	0.02	0.19	3.7	0.3	0.0	0.5
4	96.4	0.27	0.19	M13	0.09	13	11	14	0.29	-0.19	-0.27	-0.06	0.6	0.5	0.1	0.8
4	96.6	0.18	0.19	M13	-0.11	9	4	16	0.29	0.11	0.02	0.28	0.6	0.3	0.0	0.7
4	98.3	0.23	0.19	M13	-1.81	9	5	13	0.29	-0.08	-0.20	-0.02	0.6	0.2	0.0	0.4
5	4.2	0.19	0.21	M14	0.95	8	6	11	0.18	-0.06	-0.15	-0.01	0.2	0.1	0.0	0.3
5	93.4	0.36	0.26	M15	0.10	30	28	32	0.75	-0.71	-0.73	-0.68	5.0	5.3	4.9	5.6
5	94.5	0.09	0.26	M15	-1.00	22	15	32	0.75	-0.50	-0.53	-0.48	5.0	1.0	0.9	1.1

^(a)The three true major QTLs missing are:
M5 on chr. 2 at pos. 30.00 (MAF =0.21, |β_Q|=0.33, %PVE_Q =0.8),
M10 on chr. 4 at pos. 3.21 (MAF =0.39, |β_Q|=0.61, %PVE_Q =4.0),
M11 on chr. 4 at pos. 36.93 (MAF =0.24, |β_Q|=0.34, %PVE_Q =1.0).
Chr = chromosome, Pos = position in cM from the start of the chromosome, MAF = minor allele frequency, Dist = directed distance in cM of a marker to the closest true major QTL, 2 ln(BF_m) = posterior mean of the 2 ×log-transformed Bayes factor in favor of marker association, |β_Q| and E_post(β_m) = true absolute value and signed posterior mean of the additive effect size, respectively, % PVE_Q and E_post(%PVE_m) = true value and posterior mean of the percentage of variance explained, respectively.True values are taken from Table one in [18].

ISSN: 1297-9686