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Table 1 Statistics of PET characteristics

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 (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.  
  1. * 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.