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Table 3 Identified significant SNP using GRAMMAR approach.

From: Genome wide association analysis of the QTL MAS 2012 data investigating pleiotropy

trait

chr.

positiona

effectb

sec

Χ2 d

Trait 1

1

84.05

14.81

3.45

18.39***

 

1

84.10

-13.97

3.48

16.09***

 

4

24.85

-14.74

3.84

14.70***

 

4

24.90

23.06

3.47

44.23***

 

4

25.00

12.64

3.40

13.83**

 

4

25.25

13.58

3.97

11.69*

Trait 2

1

14.60

-0.96

0.19

26.20***

 

1

14.70

0.62

0.18

11.80*

 

1

14.75

0.65

0.18

12.61*

 

1

14.85

0.87

0.22

16.28***

 

3

2.15

-1.04

0.27

14.39**

 

4

24.85

-0.83

0.21

16.37***

 

4

24.90

1.40

0.19

57.50***

 

4

25.00

0.77

0.18

17.93***

 

4

25.25

0.73

0.21

11.83*

Trait 3

1

58.00

-0.0021

0.0006

13.17***

 

1

58.25

-0.0018

0.0005

10.96*

 

1

58.85

0.0013

0.0004

10.61*

 

1

84.05

-0.0025

0.0004

39.27***

 

1

84.10

0.0024

0.0004

37.30***

 

1

84.80

0.0017

0.0005

10.93*

 

1

84.90

-0.0019

0.0004

23.59***

 

2

79.15

-0.0015

0.0004

14.41***

 

2

79.20

-0.0023

0.0004

29.32***

 

3

2.15

-0.0022

0.0006

14.26***

 

3

36.85

-0.0014

0.0004

12.50**

PC 1

1

14.60

-0.07

0.02

12.98*

 

1

84.05

0.07

0.02

14.30**

 

1

84.10

-0.07

0.02

12.23*

 

4

24.85

-0.09

0.02

16.08***

 

4

24.90

0.14

0.02

49.33***

 

4

25.00

0.07

0.02

15.27**

 

4

25.25

0.08

0.02

12.42*

PC 2

1

14.60

-0.07

0.02

15.50***

 

1

14.70

0.05

0.02

10.35*

 

1

84.05

-0.09

0.02

30.50***

 

1

84.10

0.09

0.02

29.76***

 

1

84.90

-0.07

0.02

19.80***

 

2

79.15

-0.07

0.02

16.33***

 

2

79.20

-0.09

0.02

26.57***

 

3

2.15

-0.11

0.02

21.32***

 

3

2.30

-0.08

0.02

10.40*

 

3

36.85

-0.06

0.02

10.57*

  1. a: position in Mb, b: additive effect of the trait, c: standard error of the additive effect, d: chi-squared value with genome wide p-value applying 1000 permutations (***: P < 0.001; **: P < 0.01, *: < 0.05), PC: principal component