Table 1

Direct comparison of coverage statistics from exome re-sequencing (2 × 40 bp, Illumina) of four inbred strains with two exome probe pool designs, alpha and beta

Sample


C57BL/6J

C57BL/6J

129S1/SvImJ

129S1/SvImJ

BALB/cJ

BALB/cJ

C3H/HeJ

C3H/HeJ


Exome version

Alpha

Beta

Alpha

Beta

Alpha

Beta

Alpha

Beta

Quantitative PCR

161.81

168.53

129.43

95.75

168.92

165.08

168.38

92.00

Target exons

203,225

203,224

203,225

203,224

203,225

203,224

203,225

203,224

Target bases

54,367,346

54,367,244

54,367,346

54,367,244

54,367,346

54,367,244

54,367,346

54,367,244

Target bases covered

52,266,238

53,273,874

51,746,839

52,508,881

51,828,334

52,862,662

52,136,965

51,460,949

Percentage target bases covered

96.14

97.99

95.18

96.58

95.33

97.23

95.90

94.65

Target bases not covered

2,101,108

1,093,370

2,620,507

1,858,363

2,539,012

1,504,582

2,230,381

2,906,295

Percentage target bases not covered

3.86

2.01

4.82

3.42

4.67

2.77

4.10

5.35

Median coverage

18.45

20.74

17.93

16.37

18.05

20.75

18.76

7.86

Total reads

60,582,097

60,207,746

64,258,556

44,434,168

64,495,816

63,740,186

64,959,026

25,760,946

NC80

0.28

0.37

0.25

0.33

0.25

0.31

0.29

0.32

1/NC80

3.53

2.71

4.03

3.02

3.96

3.27

3.50

3.13


1/NC80 is the fold 80 penalty, which represents the fold of over-sequencing necessary to move 80% of the below median bases to median.

Fairfield et al. Genome Biology 2011 12:R86   doi:10.1186/gb-2011-12-9-r86

Open Data