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Table 1 Detection of recombination during PCR

From: Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

Sample

Fragment

Mixture

Number of sequence

  
   

Total sequence

Wild type

Mutant

Recombinant

Observed rate of recombinants

Corrected rate of recombinants

Run1

MID1

1

100% wild type

8503

8483

0

20

0.24%

0.00%

MID2

1

100% wild type

43699

43480

2

217

0.50%

0.00%

MID5

1

10% mutant

15923

12485

2039

1399

8.79%

8.42%

MID7

1

1% mutant

9548

9329

98

121

1.27%

0.90%

MID3

2

100% mutant

24210

1

24127

82

0.34%

0.00%

MID4

2

100% mutant

13466

0

13432

34

0.25%

0.00%

MID10

2

10% mutant

49169

35477

10156

3536

7.19%

6.90%

MID11

2

1% mutant

12070

11681

171

218

1.81%

1.51%

Run2

MID1

1

100% wild type

48828

48735

0

90

0.18%

0.00%

MID2a

1

100% wild type; Clone DNA/no PCR

98785

98670

2

113

0.11%

0.00%

MID5

1

100% mutant

52287

0

51903

384

0.73%

0.00%

MID7

1

50% mutant

58882

18565

31388

8929

15.16%

14.82%

MID9

1

50/50 mix RNA

54744

14151

27648

12945

23.65%

23.30%

MID3

2

100% mutant

60477

6

60297

174

0.29%

0.00%

MID4

2

100% wild type

38970

38705

0

265

0.68%

0.00%

Run 3

MID11

1

50% mutant

62437

21163

40777

497

0.78%

0.43%

MID12

1

50% mutant

122327

23589

83134

15604

12.00%

11.65%

  1. a Run2MID2: Cloned DNA without PCR amplification.