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Table 2 PET mapping to the genome

From: PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data

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

  1. * 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.