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Table 1 Comparison of PolyMin phase I, PolyMin phase I+II and BEST in their ability to detect minimum sets of polymorphisms and the usability of these polymorphism sets for genotype differentiation.

From: "PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation

Gene

Number of different haplotypes

Number of possible genotypes

Program used

Minimum number of polymorphisms

Identified genotypes

Number of non- identifiable genotypes

Number of genotype groups left

CCoAOMT- 1

12

78

A1

6

67

11

5

   

B2

5

29

49

21

   

C3

6

73*

5*

2*

   

D4

17

77

2

1

CCoAOMT-2

16

136

A1

7

128

8

4

   

B2

5

49

87

25

   

C3

6

110*

26*

12*

   

D4

43

136

0

0

COMT

30

465

A1

12

447

18

9

   

B2

8

234

231

75

   

C3

9

415*

0

24*

   

D4

74

465

50*

0

Lac1

16

136

A1

8

122

14

7

   

B2

4

19

117

16

   

C3

8

124*

12*

6*

   

D4

27

132

4

2

Lac5-4

20

210

A1

9

182

28

13

   

B2

6

51

169

45

   

C3

9

182*

28*

13*

   

D4

47

203

7

3

Lac5-6

8

36

A1

6

34

2

1

   

B2

6

34

2

1

   

C3

6

34*

2*

1*

   

D4

7

34

2

1

Ra1

12

78

A1

11

78

0

0

   

B2

11

78

0

0

   

C3

11

78*

0

0

   

D4

11

78

0

0

  1. A1 PolyMin phase I,
  2. B2 PolyMin phase I+II (= non-informative polymorphisms excluded),
  3. C3 BEST,
  4. D4PolyMin genotype differentiation optimized (= all non-redundant polymorphisms included),
  5. *The genotype differentiation for the minimum polymorphism set generated by BEST was performed with PolyMin.
  6. Example data sets where extracted from NCBI (CCoAOMT- 1: AY323241–AY323271, CCoAOMT- 2: AY279004–AY279035, COMT: AY323272–AY323305, Lac1: AY464016–AY464051, Ra1 DQ013174–DQ013202) or from Xing et al. [25].