Table 4

Comparison of M-QTL and reported QTL.

Estimated QTL

Simulated QTL

MR^f

LABayes^g

LDBayesⁱ

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

^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.

Crooks et al. BMC Proceedings 2009 3(Suppl 1):S2