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Table 1 Summary of reads assembly generated by SOAPdenovo from control and phenylalanine treated Boesenbergia rotunda callus

From: Transcriptome profiling shows gene regulation patterns in a flavonoid pathway in response to exogenous phenylalanine in Boesenbergia rotunda cell culture

  Control Phenylalanine treated
Total number of reads 24473594 23470648
Total nucleotides (nt) 3671039100 3520597200
GC% 49.31% 47.89%
Q20% 95.13% 96.06%
Step-wise assembly
  Total number of contig 287451 273979
  Average sequence size of contigs 199 191
  N50 length of contig 236 221
  Total number of scaffolds 149648 147381
  Average sequence size of scaffolds 359 330
  N50 length of scaffold 535 465
  Total number of unigenes 78998 77541
  Total nucleotides (nt) in unigenes 44279890 39284596
  Average sequence size of unigenes 561 507
  N50 length of unigenes 703 610
Combined control and phenylalanine treated unigenes
  Total number of all unigenes 101043
  Average sequence size of all unigenes 599
  N50 length of all unigenes 804
  Unigenes with orientation 54284
  Unigenes without orientation 46759
  1. N50 size of contigs, scaffolds or unigene was calculated by ordering all sequences then adding the lengths from longest to shortest until the summed length exceeded 50% of the total length of all sequences.
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BMC Genomics

ISSN: 1471-2164

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