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.