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

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

Marker Closest true
major QTL(a)
2ln(BFm)   |β Q | Epost(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
  1. (a)The three true major QTLs missing are:
  2. M5 on chr. 2 at pos. 30.00 (MAF =0.21, |β Q |=0.33, %PVE Q =0.8),
  3. M10 on chr. 4 at pos. 3.21 (MAF =0.39, |β Q |=0.61, %PVE Q =4.0),
  4. M11 on chr. 4 at pos. 36.93 (MAF =0.24, |β Q |=0.34, %PVE Q =1.0).
  5. 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 Epost(β m ) = true absolute value and signed posterior mean of the additive effect size, respectively, % PVE Q and Epost(%PVE m ) = true value and posterior mean of the percentage of variance explained, respectively.True values are taken from Table one in [18].