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Table 5 Accuracy and reliability of QSS on viral DNA extracted from an infected plant

From: Quantitative Single-letter Sequencing: a method for simultaneously monitoring numerous known allelic variants in single DNA samples

 

Replicate n°

  
 

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

Average

SD

VIT 1

42

40

42

41

41

41

40

41

41

44

42

44

44

43

43

42

43

42

43

42.0

1.3

VIT 2

5.4

5.6

5.5

5.8

5.9

6.6

6.0

5.8

6.1

4.9

5.6

5.2

5.2

5.1

5.3

6.6

5.8

5.3

5.4

5.6

0.5

VIT 3

39

36

40

38

37

39

39

40

39

41

39

41

42

42

42

38

40

42

42

39.9

1.8

VIT 4

11

12

11

11

12

11

11

11

11

9

11

9

8

9

9

11

9

9

9

10.3

1.2

VIT 5

1.4

3.3

1.1

1.9

2.5

1.3

2.2

1.3

1.2

1.1

1.4

0.6

ND

0.5

0.6

2.8

1.4

1.1

1.1

1.5

0.7

VIT 6

1.1

2.9

1.0

1.9

1.7

1.4

2.1

1.2

1.0

ND

0.7

ND

ND

ND

ND

ND

ND

ND

ND

1.5

0.6

  1. Viral DNA was extracted from a plant infected with the CaMV Mix6VIT, and processed independently 19 times for PCR amplification and QSS analysis. Average final estimates (proportionally corrected to give a total of 100% in each case) and standard deviation (SD) among repeats are shown on the right.
  2. Peaks yielded by low-frequency markers VIT 5 and VIT6, when identified, emerged just above the base line of the sequence traces. As indicated in the text, the corresponding frequency estimates reported in this table fall below the threshold of QSS accuracy, as confirmed by the high SD associated with VIT5 and VIT6, and by numerous repeats where estimates could not be obtained (ND), because the corresponding peaks were not clearly distinguishable on the electropherogram.
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BMC Genomics

ISSN: 1471-2164

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