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Table 1 SNP call accuracy and SNP call rate of 3D7 cultured parasites

From: A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity

 

SNP call accuracy

SNP call rate

 

Heuristic algorithm

D-score method

Heuristic algorithm

D-score method

WGA

+

-

+

-

+

-

+

-

LD

+

-

+

-

+

-

+

-

+

-

+

-

+

-

+

-

1,000 p/μl

99.0

96.2

99.6

94.1

93.5

76.4

97.4

69.0

75.4

36.8

68.7

15.6

56.0

40.7

63.2

32.3

10,000 p/μl

99.4

99.4

99.7

99.5

94.4

95.8

98.6

94.1

76.5

87.5

87.6

62.9

51.7

59.1

70.8

50.4

100,000 p/μl

-

99.6

-

99.7

-

98.7

-

98.8

-

94.4

-

92.0

-

76.0

-

78.9

500,000 p/μl

-

99.7

-

99.8

-

98.4

-

98.9

-

94.5

-

95.3

-

64.4

-

72.8

  1. To test the accuracy and call rate of the new heuristic algorithm cultured 3D7 strain parasites were genotyped under differing leukocyte depletion, whole-genome amplification, and parasite concentrations. We then compared the previously describe D-score method to the heuristic algorithm. (WGA = whole-genome amplification, LD = leukocyte depletion, p/μl = parasites per microliter).
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BMC Genomics

ISSN: 1471-2164

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