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Table 3 Accuracy of variant calling

From: Deep sequencing of the X chromosome reveals the proliferation history of colorectal adenomas

Sample

All mutations

4% ≤ Frequency <10%

Tested

Validated

Accuracy

Tested

Validated

Accuracy

(% total)

(% total)

A1

24 (7%)

24

100%

4 (25%)

4

100%

A2

11 (20%)

9

82%

2 (9%)

2

100%

A3

20 (12%)

17

85%

4 (6%)

2

50%

A4

14 (8%)

13

93%

3 (14%)

3

100%

Overall

69 (9%)

63

91%

13 (10%)

11

85%

  1. Mutations were randomly selected and tested with either Sanger sequencing (frequency ≥10%) or TaqMan assay (4% ≤ frequency <10%). TaqMan results for mutations with frequency <4% were inconclusive, likely due to the detection limit of the assay (see Table S1 in Additional file 1). Accuracy was estimated as the fraction of confirmed variants over the total pool of tested variants.
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Genome Biology

ISSN: 1474-760X

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