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

BMC Genomics

Table 4 Summary of assembly of all catfish expressed short reads

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

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.

ISSN: 1471-2164