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Table 1 Comparison of the prior specifications in the eight MCMC chains A-H used to analyse the QTLMAS XII data, posterior estimates of model parameters and summary statistics

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

  Prior specification Posterior mean (sd) of   
Chain p 0 b (a) N Q α 1 0 2 σ u 2 σ 2 hM2 (b) N Q
A 0.99 0.01 58.9 2.0 (0.6) 1.7 (1.2) 3.0 (0.1) 0.32 (0.02) 23.0 (2.5)
B 0.99 0.01 58.9 2.6 (0.7) 1.7 (1.2) 3.0 (0.1) 0.32 (0.02) 22.9 (2.6)
C 0.99 0.001 58.9 2.3 (0.5) 3.0 (1.9) 3.0 (0.1) 0.30 (0.02) 31.5 (2.5)
D 0.99 0.001 58.9 2.6 (0.5) 3.0 (1.9) 3.0 (0.1) 0.29 (0.02) 31.1 (2.5)
E 0.999 0.01 5.9 2.1 (0.5) 1.9 (1.3) 3.0 (0.1) 0.31 (0.02) 15.3 (1.3)
F 0.999 0.01 5.9 2.8 (0.5) 2.1 (1.4) 3.0 (0.1) 0.31 (0.02) 14.3 (1.3)
G 0.999 0.001 5.9 1.9 (0.4) 3.9 (2.3) 3.1 (0.1) 0.28 (0.02) 21.5 (1.4)
H 0.999 0.001 5.9 2.0 (0.7) 3.7 (2.2) 3.1 (0.1) 0.28 (0.02) 22.6 (1.8)
  1. (a) given in units of phenotypic standard deviations (sd(Y)=2.10).
  2. (b) The true overall heritability of the trait is 0.30 [19].
  3. Hyper-parameter p0 defines the prior probability that the effect size lies in the interval of the spike, (−b,b). N Q is a summary statistic for the number of QTL (see text for details), α the common intercept in the regression, σ u 2 the variance component of the polygenic terms, σ2 the residual variance, and h M 2 the part of the heritability due to marker effects.