Table 1

Statistics of PET characteristics

Library Type

GIS-PET

ChIP-PET

Library ID

SHC012

SHC013

(combined)

SHC016

SHC019

(combined)


Raw sequence reads

74,537

53,758

128,295

89,359

82,941

172,300

Spacer-defined PETs

741,799

363,963

1,105,762

777,038

845,045

1,622,083

PET/sequence read

10

6.8

8.6

8.7

10.2

9.4

Rejected poor PETs

157,175

83,623

240,798

51,161

81,510

132,671

Rejection rate % *

21.1

22.3

22

6.6

9.7

8.2

Total high-quality PETs

584,624

280,340

864,964

725,877

763,535

1,489,412

Total unique PETs

135,757

145,138

280,895

640,844

582,253

1,223,097

Redundancy % **

76.8

48.2

62.5

11.7

23.7

17.7

5' AT content (%)

31.71

32.89

32.30

58.06

57.85

57.96

3' AT content (%)

61.49

62.18

61.84

57.98

57.57

57.78


Breakdown of rejected PETs

157,175

83,623

240,798

51,161

81,510

132,671

Length < 34

43,022

7,942

26,343

64,900

-27.40%

-9.50%

-51.10%

-79.60%

Length > 40

17,377

7,967

24,794

16,581

-11.10%

-9.50%

-48.90%

-20.40%

Contain N

16

3

24

29

No AA-tail at 3' end

43,673

26,901

-30.00%

N. A.

N. A.

-27.80%

-32.20%

PolyA(9) in 3' tag

41,983

20,264

-25%

N. A.

N. A.

-26.70%

-24.20%

PolyA(9) in 5' tag

433

99

N. A.

N. A.

PolyT(9) in 5' tag

116

118

N. A.

N. A.

PolyT(9) in 3' tag

639

323

N. A.

N. A.


* Rejection rate = "Rejected poor PETs"/"Spacer-defined PETs". ** Redundancy = (1-Total unique PETs/Total high quality PETs) × 100. The number states the percentage of PET tags that are redundant in the category.

Chiu et al. BMC Bioinformatics 2006 7:390   doi:10.1186/1471-2105-7-390

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