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Table 1 Estimated copy numbers of template in each PCR amplification and results from the random degradation model fits.

From: Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

(a) Sea lion DNA

Sample

Mean copy number at various amplicon sizes

Model parameters

 

61 bp

91 bp

163 bp

230 bp

327 bp

λa

CV(λ)

1/λb

R2

1

44727

22461

11965

3746

1387

0.0129

10.3

78

0.92

2

24347

15968

5393

1487

525

0.0148

6.9

67

0.96

3

236825

193410

121534

44745

25936

0.0088

9.1

113

0.94

4

35346

30846

20383

9914

5390

0.0074

10.9

135

0.91

5

43789

26107

11972

4232

1276

0.0135

7.6

74

0.96

6

179118

126256

57217

26322

8684

0.0115

7.9

87

0.95

7

167038

123458

62726

17076

7944

0.0121

7.0

83

0.96

8

29683

25006

14941

9007

2818

0.0089

8.7

113

0.94

9

198820

222720

146709

53608

19759

0.0093

11.0

108

0.91

10

58503

46534

34979

25738

9624

0.0066

11.7

153

0.90

Mean

101820

83277

48782

19588

8334

0.0106

9.1

101

0.94

(b) Herring DNA

Sample

Mean copy number at various amplicon sizes

Model parameters

 

69 bp

123 bp

184 bp

226 bp

304 bp

λ a

CV(λ)

1/λ b

R 2

1

8157

522

143

93

42

0.0221

15.9

45

0.83

2

9927

994

257

240

120

0.0192

19.7

52

0.76

3

14005

2016

687

381

178

0.0179

11.2

56

0.91

4

1575

418

246

182

69

0.0123

10.9

81

0.91

5

11649

952

243

149

46

0.0222

12.5

45

0.89

6

11754

1700

605

307

120

0.0188

9.7

53

0.93

7

18588

4016

1272

1165

234

0.0180

11.7

56

0.90

8

25203

8883

2306

1366

429

0.0173

6.0

58

0.97

9

26295

5497

1299

655

266

0.0197

9.2

51

0.94

10

711

432

238

138

107

0.0086

11.9

117

0.90

Mean

12786

2543

729

468

161

0.0176

11.9

61

0.89

  1. aλ is an estimate of the probability of a nucleotide being damaged.
  2. b 1/λ is an estimate of the average undamaged fragment size (in base pairs)