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Table 3 De novo transcriptome assembly quality statistics

From: Next generation sequencing and de novo transcriptomics to study gene evolution

Gene H. annuus A. montana Z. haageana Z. haageana H. helianthoides H. helianthoides
  ws60, paired ws60, paired autows, non-paired ws60, paired autows, non-paired ws60, paired
LEA 90% 80% 97% 79% 53% 73%
  165,041 23 25,957 5,584 162,273 176,283
OLE 100% 100% 57% 95% 100% 45%
  14,242 23,511 108,400 12,436 114,811 145,334
AP 78% 100% 63% 89% 97% 97%
  1,666 405 237 43 5,704 5,704
PR 100% 100% 89% 100% 79% 100%
  4,922 6,183 6 13 44,849 36,182
CP-1 51% 72% 100% 98% 100% 94%
  122 44 70 66 363 355
PK 73% 63% 83% 97% 75% 99%
  63 48 59 40 175 229
PawS1a 100% - 100% 100% 70% 70%
  532   3,862 3,362 1,827 1,827
PawS1b 84% - 79% 100% 32% 40%
  221   809 927 88 86
PawS1c - - 29% 58% 32% 41%
    15 58 798 782
PawS1d - - 70% 41% - -
    19,930 7,916   
PawS1e - - 33% 36% - -
    2,236 7,394   
PawS1f - - 33% 42% - -
    2,142 2,518   
PawS1g - - 44% - - -
    7,071    
PawS1h - - - 37% - -
     129   
PawS1i - - 30% - - -
    550    
PawS1j - - - 40% - -
     30   
PawS1k - - 22% 52% - -
    4 8690   
PawL1a 98% 100% 100% - 100% 100%
  25 400 4   4,711 4,711
PawL1b - - 40% 87% - -
    4,125 4,736   
  1. All four species were assembled with word size (ws) 60, paired method. In addition, Z. haageana and H. helianthoides transcriptomes were assembled with the automatic word size (autows, 23), non-paired method. The first line shows the percentage coverage of the identified transcripts when compared to the expected full length protein query. The second line shows the average coverage by mapping trimmed, filtered reads on identified full/partial transcripts. Average coverage means sum of the bases of the aligned part of all the reads divided by the length of the reference sequence.