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Table 4 Variant discovery and HapMap concordance for different sequencing types and varying amounts of sequence data

From: Whole exome capture in solution with 3 Gbp of data

 

Illumina

SOLiD

 

Frag

PE

PE (high stringency)

1

1

Bases produced (Gbp)

2.51

2.84

 

3.4

9.99

Bases on target after duplicate removal (Gbp)

1.04

2.01

 

0.59

1.72

Total SNPs

21,239

27,953

26,489

19,790

24,077

dbSNP SNPs

19,525

23,745

23,133

18,016

21,350

dbSNP (%)

91.9

84.95

87.3

91.04

88.67

HapMap variant concordance (%)

83.0

96.0

95.8

81.6

92.9

Variant concordance (>9× coverage) (%)

95.5

98.5

98.2

94.5

97.2