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Table 4 Comparison of M-QTL and reported QTL.

From: Comparison of analyses of the QTLMAS XII common dataset. II: genome-wide association and fine mapping

Simulated QTL Estimated QTL
MR f LABayes g LDBayes i LDLA1 j LDMulti LDHap LDLA2
QTL Chr a Loc b e c p d Vg e e Loc e h Loc e h Loc e k Loc e k Loc e h Loc Vg
M1 1 20.0 0.62 0.28 11.8 0.61 21 0.55 19.5 0.66 23.2 -l 19.6 0.31 20.0 0.71 19.5 0.12
M2 1 40.0 0.56 0.07 3.1 0.62 41 0.67 39.3 0.59 41.5 0.41 40.2 0.12 40.2 0.78   
M3 1 77.2 0.37 0.29 4.4 0.42 76 0.30 77.7 0.48    77.8 0.23 77.8 0.40 76.6 0.04
M4 2 27.4 0.35 0.44 4.7 0.44    24.9 0.43    27.0 0.22 26.7 0.43 26.0 0.12
M5 2 30.0 0.33 0.21 2.8 0.25 29 0.58    32.6 0.22       
M6 2 48.6 0.37 0.40 5.1 0.39 50 0.46 48.2 0.42 48.3 0.29 48.3 0.18 48.7 0.45 53.2 0.10
M7 2 74.9 0.50 0.18 5.5 0.46             
M8 3 14.9 0.30 0.40 3.3 0.27        13.3 0.16 13.3 0.35 11.9 0.07
M9 3 60.0 0.68 0.07 4.4 0.70          60.1 -l   
M10 4 3.2 0.61 0.39 13.6 0.64 4 0.78 3.4 0.55 3.3 0.49 3.3 0.33 3.2 0.59 3.1 0.49
M11 4 36.9 0.34 0.24 3.2 0.37    36.3 0.40         
M12 4 76.1 0.58 0.41 12.5 0.57 77 0.50 76.5 0.52 76.5 0.50 76.5 0.24 76.5 0.55   
M13 4 96.5 0.29 0.19 2.0 0.39 98 0.41 99.2 0.4 96.5 0.32    95.2 -l   
M14 5 5.1 0.18 0.21 0.8 0.25 2 0.35           
M15 5 93.5 0.75 0.26 16.8 0.75 95 0.72 95.5 0.6    93.5 0.36 93.5 0.63 93.9 0.18
  1. aChromosome. bLocation. cAverage effect of allelic substitution (absolute value). dMinor allele frequency. ePercentage of genetic variance explained by the QTL. fMultiple regression on known QTL genotypes. gOne QTL was falsely identified at 10 cM on chromosome 4. hReported estimate of the additive effect. iOnly the positions with the 16 largest effect estimates were included. Five QTL were falsely identified at 52.6 cM on chromosome 1, 65.4 cM on chromosome 3, and 3.0, 3.7 and 75.8 cM on chromosome 4. jTwo QTL were falsely identified at 3.1 and 4.8 cM on chromosome 4. kHalf the difference between the estimated genotypic value of the 22 and 11 genotypes. lNot estimated.