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Table 3 Second major higher-order interaction. L o g 10-transformed means for the 5-way interaction between assembly, mapper, variant caller, MAPQ and read length

From: An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

   

Length

50

100

150

300

500

1000

Assembly

Mapper

Variant caller

MAPQ

      

Allpaths

Bowtie2

FreeBayes

0

3.75

3.81

3.84

4.00

3.90

3.95

Allpaths

BWA

FreeBayes

0

3.68

3.72

3.75

3.77

3.77

3.73

Allpaths

Bowtie2

GATK

0

3.34

3.37

3.45

3.61

3.53

3.65

Allpaths

BWA

GATK

0

1.74

1.78

1.84

1.90

1.91

1.96

Control

Bowtie2

FreeBayes

0

0.00

0.00

0.00

2.76

0.63

0.08

Control

BWA

FreeBayes

0

2.80

1.98

1.33

0.52

0.08

0.44

Control

Bowtie2

GATK

0

0.00

0.00

0.00

2.05

0.29

0.15

Control

BWA

GATK

0

0.00

0.00

0.00

0.00

0.00

0.00

Velvet

Bowtie2

FreeBayes

0

3.65

3.82

3.88

4.10

3.92

3.92

Velvet

BWA

FreeBayes

0

3.61

3.64

3.71

3.76

3.76

3.75

Velvet

Bowtie2

GATK

0

2.40

3.08

3.27

3.60

3.41

3.57

Velvet

BWA

GATK

0

1.14

1.48

1.62

1.70

1.78

1.85

Allpaths

Bowtie2

FreeBayes

20

3.26

3.34

3.42

3.61

3.57

3.68

Allpaths

BWA

FreeBayes

20

1.72

1.77

1.81

1.87

1.89

1.90

Allpaths

Bowtie2

GATK

20

3.50

3.56

3.62

3.76

3.65

3.74

Allpaths

BWA

GATK

20

1.87

1.92

1.96

2.01

2.00

2.02

Control

Bowtie2

FreeBayes

20

0.00

0.00

0.00

1.95

1.34

1.23

Control

BWA

FreeBayes

20

0.00

0.00

0.00

0.00

0.00

0.00

Control

Bowtie2

GATK

20

0.00

0.00

0.00

2.15

1.16

1.02

Control

BWA

GATK

20

0.00

0.00

0.00

0.00

0.00

0.00

Velvet

Bowtie2

FreeBayes

20

2.48

3.12

3.34

3.64

3.54

3.66

Velvet

BWA

FreeBayes

20

1.20

1.50

1.64

1.74

1.80

1.85

Velvet

Bowtie2

GATK

20

2.52

3.17

3.37

3.69

3.52

3.67

Velvet

BWA

GATK

20

1.24

1.52

1.66

1.75

1.84

1.90

Sed = 0.02191

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