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Table 2 Mapping statistics

From: Novel insights into the insect trancriptome response to a natural DNA virus

  SOAP transdenovo Trinity
  kmer size =25 % kmer size=31 % Edge threshold =0.05 % Edge threshold =0.16 %
Total # of fragments 376,604,607   376,604,607   376,604,607   376,604,607  
Total # of mapping fragments 345,067,834 91.63 356,499,243 94.66 351,206,829 93.26 368,474,636 97.84
# of chr in reference 80,425   82,753   135,990   127,665  
Uniquely mapping pairs         
Concordant 236,768,017 68.61 252,262,424 70.76 240,006,041 68.34 260,088,477 70.59
Halfmapping 10,181,639 2.95 10,833,441 3.04 4,222,926 1.20 3,128,004 0.85
unpaired 1,674,474 0.49 2,975,582 0.83 758,404 0.22 925,244 0.25
Multiply mapping pairs         
Concordant 93,559,753 27.11 87,279,976 24.48 103,451,332 29.46 100,980,778 27.41
halfmapping 2,102,511 0.61 2,270,699 0.64 1,287,909 0.37 1,710,051 0.46
unpaired 581,342 0.17 611,289 0.17 1,240,292 0.35 1,256,968 0.34
Translocated read pairs         
concordant 0   0   0   0  
Halfmapping 0   0   0   0  
unpaired 0   0   0   0  
Others         
paired multimapping 35,508 0.01 33,876 0.01 48,569 0.01 53,351 0.01
paired unique inverted 116,861 0.03 84,905 0.02 65,638 0.02 71,371 0.02
paired unique long 25,618 0.01 50,100 0.01 7,667 0.00 8,165 0.00
paired unique scr 22,111 0.01 96,951 0.03 118,051 0.03 252,227 0.07
No mapping 31,536,773 9.14 20,105,364 5.64 25,397,778 7.23 8,129,971 2.21