Skip to main content

Table 3 Summary of de novo assembly of the unassembled expressed short reads from reference assembly of channel catfish and blue catfish

From: Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

Catfish species

No. of reads used for assembly

No. of reads assembled

% sequences assembled

No. of contigs

Average contig length (bp)

Average contig size*

Average coverage#

Channel

66.2 × 106

46.8 × 106

70.7%

420,165

298

111

19.7

Blue

90.8 × 106

64.3 × 106

70.8%

420,953

315

153

26.4

  1. All the newly generated expressed short reads were first assembled using reference assembly (Table 2), and those that were not assembled, i.e., they did not align in silico to the existing catfish ESTs, were used for the de novo assembly. *Number of reads per contig. #Total number of assembled read bases/Total number of bases in consensus sequence.