Table 2

Inferred frequencies of haplotypes.

SNP

Haplotype Frequency



-476

-339

-308

-301

-278

-168

-75

-57

-31

-6

-1

3

16

25

59

Empirical

Phase, no LD

Phase, with LD

Haplotyper

PL-EM

SNPHAP


Empirical Haplotypes

1

G

G

G

G

G

T

A

T

G

A

A

G

A

A

T

0.334

0.312

0.321

0.325

0.333

0.326

2

G

G

G

G

T

T

A

G

G

G

A

G

A

A

T

0.162

0.166

0.162

0.166

0.181

0.171

3

G

G

T

T

G

T

A

G

G

A

A

G

A

A

T

0.091

0.097

0.097

0.101

0.098

0.102

4

G

G

T

T

G

T

A

G

-

A

A

G

A

A

T

0.052

0.055

0.055

0.049

0.047

0.050

5

G

G

G

G

T

T

G

G

G

G

A

G

A

A

T

0.042

0.052

0.052

0.052

0.049

0.050

6

G

G

T

T

G

T

A

G

-

A

A

G

A

A

G

0.029

0.032

0.032

0.032

0.030

0.030

7

G

G

G

G

T

T

A

G

G

G

T

G

A

A

T

0.026

0.032

0.032

0.032

0.028

0.029

8

G

G

T

T

G

T

A

G

G

G

A

G

A

A

T

0.019

0.016

0.016

0.013

0.016

0.018

9

G

G

G

G

T

T

A

T

G

G

A

G

A

A

T

0.019

0.013

0.013

0.013

0.011

0.011

10

G

G

T

T

G

T

A

G

-

G

A

G

A

A

T

0.019

0.023

0.026

0.023

0.025

0.025

11

G

G

G

G

T

T

G

G

G

G

A

G

G

C

T

0.016

0.016

0.016

0.016

0.014

0.014

12

G

G

G

G

T

T

A

G

G

A

A

G

A

A

T

0.016

0.010

0.006

0.006

0.008

0.008

13

G

-

G

G

T

T

G

G

G

G

A

G

A

A

T

0.016

0.016

0.016

0.013

0.010

0.013

14

G

G

G

G

T

C

A

G

G

G

T

G

A

A

T

0.016

0.016

0.016

0.016

0.016

0.016

15

G

G

T

T

G

T

A

G

G

G

T

G

A

A

T

0.013

0.010

0.010

0.010

0.006

0.009

16

G

G

G

G

T

T

G

G

G

A

A

G

A

A

T

0.013

0.013

0.013

0.016

0.008

0.008

17

G

-

G

G

T

T

A

G

G

G

A

G

A

A

T

0.013

0.013

0.013

0.013

0.011

0.011

18

G

G

G

G

T

T

A

G

-

G

A

G

A

A

T

0.010

-

0.006

0.010

0.007

0.008

19

A

G

G

G

T

T

A

G

G

G

A

G

A

A

T

0.010

0.013

0.013

0.010

0.005

0.010

20

G

G

G

G

G

T

A

G

-

A

A

G

A

A

T

0.010

-

0.003

0.010

0.006

0.005

21

G

G

G

G

T

T

G

G

G

G

A

G

A

A

G

0.010

0.010

0.010

0.010

0.011

0.011

22

G

G

T

T

G

T

A

T

G

A

A

G

A

A

T

0.010

0.013

0.010

0.013

0.007

0.007

23

G

G

G

G

G

T

A

G

G

A

A

G

A

A

T

0.006

0.016

0.013

0.006

0.006

0.008

24

G

G

T

T

G

T

G

G

-

A

A

G

A

A

T

0.006

-

-

-

-

-

25

G

G

T

T

G

T

A

G

G

A

A

G

A

A

G

0.003

-

-

-

0.004

0.004

26

G

G

G

G

T

T

G

G

G

G

T

G

A

A

T

0.003

0.006

0.006

0.006

0.007

0.007

27

G

G

G

G

T

T

A

T

G

A

A

G

A

A

T

0.003

0.003

0.003

-

-

-

28

G

G

G

G

T

T

A

G

-

A

A

G

A

A

T

0.003

-

-

-

-

-

29

A

G

G

G

T

T

A

G

G

A

A

G

A

A

T

0.003

-

-

-

-

-

30

G

-

G

G

T

T

A

G

G

A

A

G

A

A

T

0.003

0.003

0.003

0.003

0.003

0.003

31

G

G

G

G

T

T

G

G

-

G

A

G

A

A

T

0.003

0.010

-

-

-

-

32

G

G

T

T

G

T

G

G

G

G

A

G

A

A

G

0.003

-

-

-

0.002

-

33

G

G

G

G

T

T

A

G

G

G

A

G

G

C

T

0.003

0.003

0.003

0.003

0.004

0.004

34

G

-

G

G

T

C

A

G

G

G

T

G

A

A

T

0.003

0.003

0.003

0.003

0.003

0.003

35

G

G

G

G

G

T

A

G

G

A

C

C

A

A

T

0.003

-

-

0.003

0.003

0.003

36

G

G

G

G

T

T

A

G

G

G

T

G

A

A

G

0.003

-

-

-

0.003

0.003

Incorrect Haplotypes

1

G

-

G

G

T

T

G

G

G

G

A

G

G

C

T

-

-

-

0.002

0.002

2

G

G

G

G

T

T

G

G

-

A

A

G

A

A

T

-

0.006

-

0.009

0.008

3

G

G

G

G

T

T

G

T

-

G

A

G

A

A

T

-

-

-

-

0.002

4

G

-

G

G

T

T

G

T

G

A

A

G

A

A

T

-

-

0.003

-

-

5

G

-

G

G

T

T

G

T

G

G

A

G

A

A

T

-

-

-

0.003

0.002

6

G

G

G

G

T

T

G

T

G

G

A

G

A

A

T

-

0.003

-

-

-

7

G

G

G

G

T

T

G

T

G

A

A

G

A

A

T

-

-

-

-

0.004

8

A

G

G

G

T

T

A

T

G

A

A

G

A

A

T

-

-

0.003

0.003

0.003

9

G

G

G

G

T

T

A

G

G

G

C

C

A

A

T

0.003

0.003

-

-

-

10

A

G

T

T

G

T

A

G

-

A

A

G

A

A

T

-

-

-

0.002

-

11

A

G

T

T

G

T

A

G

G

G

T

G

A

A

T

-

-

-

0.003

-

12

G

G

T

T

T

T

G

G

-

G

A

G

A

A

T

-

-

0.006

0.004

-

13

G

G

T

T

T

T

G

G

G

A

A

G

A

A

T

-

-

-

0.003

-

14

G

G

G

G

G

T

A

T

-

A

A

G

A

A

T

0.010

-

-

-

-

15

G

G

G

G

G

T

A

T

G

G

A

G

A

A

T

0.006

0.006

0.006

0.008

0.008

16

G

G

G

G

G

T

A

T

G

A

A

G

A

A

G

0.006

0.006

0.006

-

-

Minor Allele Frequency

0.013

0.036

0.247

0.247

0.399

0.019

0.114

0.367

0.133

0.412

0.065

0.003

0.019

0.019

0.049


Adkins BMC Genetics 2004 5:22   doi:10.1186/1471-2156-5-22

Open Data