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Table 2 Characteristics of the Douglas-fir transcriptome assembly using Newbler v2.3

From: A SNP resource for Douglas-fir: de novotranscriptome assembly and SNP detection and validation

   Length (nt)
Statistic Number Mean Median N50 Total
Reads used by Newbler* 2,764,549 360 392 416 996,614,802
Reads assembled by Newbler 2,544,087 364 394 416 925,577,338
Isotigs§ 38,589 1390 1141 1883 53,622,767
Isogroups 25,002 1443 1181 1864 36,069,331
 Isogroups with 1 isotig (I1) 18,774 1334 1053 1750 25,046,862
 Isogroups with >1 isotig (IM) 6228 1770 1547 2141 11,022,469
Singletons 102,623 356 384 413 36,504,221
Total (isogroups + singletons) 127,625 569 413 517 72,573,552
  1. * The input number of reads is less than the total in Table 1 (2.96 × 106) because reads shorter than 50 nt were excluded. Statistics were calculated using the sequences actually used in the assembly after applying a default minimum length of 40 for reads trimmed by Newbler.
  2. Includes reads that assembled as complete reads or as partial reads.
  3. § Isotigs ≥ 200 nt were deposited at DDBJ/EMBL/GenBank under accession GAEK01000000.
  4. Statistics for the IM isogroups were calculated using the longest isotig in each isogroup.