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Botanical Studies

Table 1 454 Pyrosequencing results for the pepper ( Capsicum annuum ) varieties, Saengryeg 211 and Saengryeg 213

From: De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213

454 pyrosequencing terms Saengryeg 211 Saengryeg 213
Reads   
 The Number of raw sequencing reads (n) 361,671 274,269
 Bases of raw sequencing reads (bp) 164,494,414 124,608,071
 The average of read length (bp) 454,818 454,328
 Assembleda 282,705 217,905
 Partialb 50,330 33,427
 Singletonsc 18,147 15,129
 Repeatd 111 242
 Outliere 5,075 3,699
 Too shortf 5,273 3,831
 The number of bases, Q20 ≤ (bp)g 93,272,495 70,812,087
 The number of reads, Q20 ≤ (n) 269,198 205,166
Isotigs   
 Number of isotigs (n) 23,821 17,813
 Average count of contigs in the isotigs (n) 1.401 1.317
 Largest count of contigs in the isotigs (n) 12 16
 The number of isotigs assembled by one contig (n) 18,363 14,556
 The total number of bases in the isotig (bp) 20,787,054 14,965,217
 The average isotig size (n) 872.636 840.129
 N50 isotig size (bp)h 1,028 977
 The size of the largest isotig (bp) 17,462 7,300
Singletons   
 Number of singletons after SeqClean (minimum length, 100) 18,147 15,129
 Number of singletons after Lucy (minimum length, 100) 17,054 14,310
 Number of valid singletons after Lucy 16,958 14,244
  1. aThe number of read’s bases used in the assembly computation.
  2. bOnly part of the read was included in the assembly.
  3. cThe read did not overlap with any other reads in the input.
  4. dThe read deemed to be from repeat regions.
  5. eThe read was identified by the GS De Novo Assembler as problematic.
  6. fThe read was too short to be used in the computation.
  7. gThe quality of read was higher than or equal to 20.
  8. hHalf of all bases reside in contigs of this size or longer.
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