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Table 2 Examples of ML analysis, showing copy numbers in the range 2-10

From: Accurate measurement of gene copy number for human alpha-defensin DEFA1A3

    

Relative likelihood values for

   

Measured value

N = 2

N = 3

N = 4

N = 5

N = 6

N = 7

N = 8

N = 9

N = 10

Sample

NA12751

PRT1 (MLT1A0)

7.07

1.28E-139

2.84E-40

1.50E-11

6.82E-04

0.276

1

0.471

0.091

0.012

MLCN

7

PRT2 (DEFA4)

7.03

2.15E-137

1.97E-39

2.37E-07

0.010

0.458

1

0.544

0.156

0.034

Minimum ratio 511.47

indel5

1.32

0.044

2.02E-03

0.044

0.318

0.044

0.880

0.068

1

0.318

  

DefHae3

2.38

5.67E-30

0.099

0.626

0.038

0.099

0.983

0.626

0.172

0.734

  

7bpdup

2.43

6.06E-06

0.343

0.155

6.25E-03

0.343

1

0.155

0.343

0.970

  

Combined

 

4.87E-312

4.41E-83

1.76E-20

6.14E-10

2.20E-04

1

1.96E-03

9.67E-04

1.10E-04

    

N = 2

N = 3

N = 4

N = 5

N = 6

N = 7

N = 8

N = 9

N = 10

Sample

NA12749

PRT1 (MLT1A0)

5.71

6.56E-75

4.43E-18

5.99E-04

0.538

1

0.201

0.019

1.44E-03

1.16E-04

MLCN

5

PRT2 (DEFA4)

5.21

3.29E-56

3.55E-12

0.102

1

0.527

0.095

0.012

1.50E-03

2.00E-04

Minimum ratio 21.99

indel5

(-)

1

1

1

1

1

1

1

1

1

  

DefHae3

3.70

2.95E-106

1.49E-12

0.045

1

0.366

0.057

0.045

0.550

1

  

7bpdup

3.74

9.24E-114

4.16E-12

0.124

0.873

0.111

7.28E-03

0.124

0.863

0.873

  

Combined

 

0

2.08E-52

7.25E-07

1

0.045

1.68E-05

2.72E-06

2.19E-06

4.31E-08

    

N = 2

N = 3

N = 4

N = 5

N = 6

N = 7

N = 8

N = 9

N = 10

Sample

C0157

PRT1 (MLT1A0)

9.09

1.22E-272

1.34E-89

9.08E-31

2.19E-13

9.13E-06

0.022

0.478

1

0.612

MLCN

9

PRT2 (DEFA4)

9.02

3.54E-267

1.78E-87

3.73E-19

8.65E-09

5.47E-04

0.086

0.650

1

0.649

Minimum ratio 10.50

indel5

1.18

0.503

1.62E-04

0.503

0.058

0.503

0.329

0.503

0.637

0.503

  

DefHae3

6.12

0

1.88E-63

6.26E-18

7.72E-06

0.053

0.734

0.958

0.486

0.171

  

7bpdup

0.78

0.194

1.54E-05

0.194

0.351

0.194

0.938

0.194

0.985

0.351

  

Combined

 

0

3.66E-247

6.79E-67

9.71E-28

8.54E-11

1.37E-03

0.095

1

0.039

  1. Detailed examples of maximum likelihood analysis from samples NA12751 (7 copies), C0157 (9 copies) and NA12749 (5 copies) – see also Table 1. Although our analysis evaluates probabilities associated with copy numbers up to 16, for clarity we only show values up to 10 here. For sample NA12749, note that the absence of an indel5 ratio provides no information about likely copy numbers, and so all copy numbers are assigned an equal relative probability. The DEFA1:DEFA3 ratio for NA12749 is most consistent with a copy number of 5, so that (on the basis of this measure alone) a copy number of 10 is equally well supported. Probabilities below about 10-308 are rounded to zero (see Additional file 1).
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