Table 2

PET mapping to the genome

Library Type

GIS-PET

ChIP-PET

Library ID

SHC012

SHC013

SHC016

SHC019


Unique PETs

135,757

145,138

640,844

582,253

Un-mapped PET

33,097

34,648

183,314

166,764

(un-mapping rate %)

24.4

23.4

28.6

28.6

Mapped PET

102,660

110,490

457,530

415,489

(mapping rate %)

75.6

76.1

71.4

71.4

PETs mapped to one location (PET1)

83,089

88,850

422,145

382,788

(PET1 rate% to unique PETs)

61.2

61.2

65.9

65.7

(PET1 rate % to mapped PETs)

80.9

80.4

92.3

92.1

(PET1 tag total counts)

372,937

174,443

473,224

516,453

(PET1 redundancy %)*

77.7

49.1

12.1

24.3

PET1 mapped to known genes

78,905

85,031

NA

NA

(PET1 rate % to known genes)

93.6

94.3

NA

NA


PETs mapped to multiple locations (% to all mapped PETs)

PET2 (%)

7.67

8.16

1.87

1.94

PET3 (%)

2.33

2.37

0.68

0.71

PET4 (%)

1.2

1.26

0.41

0.44

PET5 (%)

0.64

0.72

0.29

0.28

PET6 (%)

0.43

0.48

0.23

0.2

PET7 (%)

0.31

0.31

0.17

0.17

PET8 (%)

0.18

0.18

0.15

0.15

PET9 (%)

0.16

0.15

0.11

0.12

PET10 (%)

0.11

0.11

0.09

0.09

PET11+ (%)

1.38

1.17

1.52

1.53


* PET1 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

Open Data