Table 2

Position of the interruption in imperfect SSR.

Homopolymers


Repeat Size

End (obs)

Middle (obs)

End (exp)

Middle (exp)

p-value


3

15,005

50

10,037

5,018

0

4

5,793

1,392

3,593

3,593

0

5

2,549

1,168

1,487

2,230

5.E-277

6

1,309

735

681

1,363

1.E-190

7

810

492

372

930

5.E-159

8

447

294

185

556

3.E-109

9

459

253

158

554

7.E-162

10

350

285

127

508

2.E-108

11

178

191

67

302

1.E-50

12

119

167

48

238

1.E-29

13

65

121

29

157

1.E-13

14

45

107

22

130

7.E-08

15

34

77

15

96

8.E-08

16

18

43

8

53

6.E-05

17

12

40

6

46

1.E-02

18

6

28

4

30

2.E-01

19

3

23

3

23

9.E-01

20

6

15

2

19

5.E-03


Dimers


Repeat Size

End (obs)

Middle (obs)

End (exp)

Middle (exp)

p-value


3

1,588

641

1,486

743

5.E-06

4

332

208

270

270

9.E-08

5

121

83

82

122

2.E-08

6

65

61

42

84

1.E-05

7

58

53

32

79

3.E-08

8

47

29

19

57

1.E-13

9

39

30

15

54

7.E-12

10

17

10

5

22

2.E-08

11

11

7

3

15

2.E-06

12

9

7

3

13

2.E-05

13

7

4

2

9

9.E-06


This table shows the position of interruptions in simple sequence repeats. "End" indicates polymorphism at beginning or end of SSR loci, while middle variation indicates polymorphism occurs at interior positions (eg. Homopolymer with repeat length of three has two possible end nucleotide positions and one possible middle position. P-value is determined using Pearson's chi-square test for random expectation.

Sung et al. BMC Genomics 2010 11:691   doi:10.1186/1471-2164-11-691

Open Data