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Table 2 Power in simulated data

From: Investigation of altering single-nucleotide polymorphism density on the power to detect trait loci and frequency of false positive in nonparametric linkage analyses of qualitative traits

Trait

Marker set

Pop. dz. freq.

Percentage of replicates with p-value belowa

   

0.05

0.01

0.0017

0.001

0.0001

0.000049

Dominant

        

   D8044

MS 7.5 cM

0.06

0.96

0.89

0.67

0.57

0.27

0.16

 

SNP 3 cM

 

0.95

0.86

0.60

0.51

0.18

0.12

 

SNP 1 cM

 

0.98

0.90

0.72

0.63

0.29

0.21

 

SNP 0.3 cM

 

0.96

0.92

0.77

0.69

0.37

0.27

   D8050

MS 7.5 cM

0.18

1.00

1.00

0.99

0.99

0.97

0.94

 

SNP 3 cM

 

1.00

1.00

0.99

0.99

0.93

0.91

 

SNP 1 cM

 

1.00

1.00

1.00

1.00

0.98

0.98

 

SNP 0.3 cM

 

0.99

0.99

0.99

0.99

0.97

0.96

   D8051

MS 7.5 cM

0.50

0.99

0.95

0.88

0.83

0.62

0.54

 

SNP 3 cM

 

0.99

0.95

0.85

0.81

0.59

0.51

 

SNP 1 cM

 

1.00

0.97

0.90

0.88

0.70

0.61

 

SNP 0.3 cM

 

1.00

0.98

0.92

0.9

0.77

0.70

Recessive

        

   R8045

MS 7.5 cM

0.08

0.99

0.93

0.74

0.67

0.32

0.22

 

SNP 3 cM

 

0.98

0.89

0.69

0.61

0.24

0.15

 

SNP 1 cM

 

0.99

0.95

0.78

0.73

0.36

0.26

 

SNP 0.3 cM

 

0.98

0.95

0.84

0.78

0.44

0.34

   R8050

MS 7.5 cM

0.01

0.46

0.10

0.005

0

0

0

 

SNP 3 cM

 

0.41

0.05

0

0

0

0

 

SNP 1 cM

 

0.79

0.45

0.13

0.004

0

0

 

SNP 0.3 cM

 

0.47

0.13

0.005

0.005

0

0

   R8051

MS 7.5 cM

0.22

1.00

1.00

0.96

0.94

0.83

0.78

 

SNP 3 cM

 

1.00

1.00

0.94

0.92

0.81

0.74

 

SNP 1 cM

 

1.00

1.00

0.98

0.98

0.88

0.85

 

SNP 0.3 cM

 

0.99

0.99

0.99

0.98

0.90

0.88

  1. aPercentage of replicates with p-value below the following criteria within a 20 cM range of the given "true" trait locus. The results were summarized across the 3 simulated populations. Each population was analyzed separately.