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Table 3 DEFB copy numbers per diploid genome estimated by the ratio of 454 haplotype calls (run 1) in comparison to alternative methods.

From: Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

 

454

Alternative methods

Amplicon

F2

F5 f

F5 r

F4

F6

F7

F8

Average

Armour

5PRT

PPRT

MLPA

Average

454-Altern.

MSVs

1-2

6-8

7-10a

3-5

11-15

16-18

19-24

 

~

     

~

~

C0140

5

 

4

 

4 (2n)

4

4

4.20

4

4

3.78

4.19

4

3.99

4

0

C0766

3

3

3

4

   

3.25

3

3

2.75

3.31

3

3.01

3

0

C0913

3

3

3

3

3

  

3.00

3

3

3.00

3.13

3

3.03

3

0

NA12760

7

6

6

6

5

6 (2n)

6 (2n)

6.00

6

6

5.57

6.04

6

5.90

6

0

NA15029

6 (3n)

5

5

6

5

5

5

5.29

5

nd

4.70

5.58

5

5.09

5

0

NA15213

5

5

4

5

4

5

5

4.71

5

nd

4.18

4.18

4

4.12

4

+1

NA15385

5

7

5

7

5

6 (2n)

5

5.71

6

nd

5.29

5.17

5

5.15

5

+1

NA18502

10

10

9

 

7

9 (3n)

8 (4n)

8.83

9

8

8.98

nd

9

8.66

9

0

NA18552

 

5

6 (2n)

7

   

6.00

6

2

2.23

2.02

2

2.06

2

+4

NA18858

4

 

4

3

 

4

5

4.00

4

8

7.71

8.08

8

7.95

8

-4

NA19140

7

 

7

 

5

6

 

6.25

6

7

5.71

6.26

6

6.24

6

0

  1. Armour: PRT and MAPH/REDVR [36] and personal communication; 5PRT. PPRT [18, 28]; MLPA [28]. ~: rounded; n: multiple of the minimal estimated CN; *: CN estimations based on ultra-deep 454 sequencing; nd: no data; blank: non polymorphic.