Table 3

Missing data. Rate of missing data per valid segregating SNP according to classes of GenTrain scores for each of white spruce and black spruce.

Species

Class of GenTrain scores

Number of SNPs assayed

Number of segregating SNPs

Number of monomorphic SNPs

Average number of missing data per SNP scored

Average call rate per SNP scored (%)1


White spruce

<0.25

165

0

0

-

-

0.25–0.3

0

0

0

-

-

0.3–0.4

3

3

0

11.0

96.2

0.4–0.5

15

10

5

2.2

99.2

0.5–0.6

46

33

13

1.9

99.3

0.6–0.7

92

81

11

1.4

99.5

0.7–0.8

323

302

21

1.6

99.4

0.8–0.9

118

82

36

2.4

99.1

>0.90

6

5

1

2.8

100

Total

768

516

87

-

-

Weighted average

-

-

-

1.8

99.4

Black spruce

<0.25

138

0

0

-

-

0.25–0.3

0

0

0

-

-

0.3–0.4

10

10

0

3.5

98.8

0.4–0.5

17

16

1

4.5

98.4

0.5–0.6

80

74

6

1.9

99.3

0.6–0.7

79

72

6

2.3

99.3

0.7–0.8

170

163

7

0.7

99.8

0.8–0.9

260

244

16

0.5

99.8

>0.90

14

13

1

2.0

99.3

Total

768

592

31

-

-

Weighted average

-

-

-

1.1

99.6


1 Average call rate is 100% minus average number of missing data in %.

Pavy et al. BMC Genomics 2008 9:21   doi:10.1186/1471-2164-9-21

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