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Table 4 Summary of assembly of all catfish expressed short reads

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

Assembly No. of reads used for assembly No. of reads assembled % sequences assembled No. of contigs Avg. contig length Max length No. of large contigs (>1 kb) Avg. contig size* Avg. coverage#
Reference1 493.4 × 106 336.0 × 106 68.1% 104,870 686 6,849 17,756 3,204 330.8
De novo 2 157.4 × 106 107.2 × 106 68.2% 421,229 340 4,615 4,133 255 44.1
  1. 1All expressed short reads from both channel catfish and blue catfish were first assembled using existing ESTs as references. 2Those that were not assembled into contigs with the reference ESTs were then assembled de novo. *Number of reads per contig. #Total number of assembled read bases/Total number of bases in consensus sequence.