Table 2 Detection of SNV and indel variants from NA12878

From: A robust targeted sequencing approach for low input and variable quality DNA from clinical samples

DNA input (ng)

Replicate number

TP

FN

% of expected

Average per input amount

Standard deviation per input amount

300

1

131

6

0.96

0.96

0.01

2

129

8

0.94

3

131

6

0.96

4

129

8

0.94

100

1

126

11

0.92

0.92

0.01

2

129

8

0.94

3

129

8

0.94

4

128

9

0.93

30

1

125

12

0.91

0.91

0.02

2

122

15

0.89

3

126

11

0.92

4

128

9

0.93

10

1

102

35

0.74

0.74

0.04

2

113

24

0.82

3

100

37

0.73

4

107

30

0.78

  1. All variants (N = 137). TP true positives, the variants in the call set that match the variants in ground truth list for the reference material available for Genome in a Bottle (GIAB) sample HG00, v 3.3.2., see Methods; FN false negatives, the variants that are in the ground truth list, but not present in the call set; FP false positives, variants in the call set that are not present in the ground truth list
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