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

BMC Genomics

Table 7 Quality SNPs selected from the putative SNPs with a set of criteria as described in the Methods section

	Intra-specific SNPs		Inter-specific SNPs³
	Channel catfish¹	Blue catfish²
Total SNPs	342,104	366,269	420,727
Transitions	208,517	230,031	262,048
Transversions	133,587	136,238	158,679
No. of contigs with SNPs	168,458	190,197	232,972
No. of contigs with Uniprot hits & SNPs	28,067	30,376	32,515
No. of unique known genes containing SNPs	16,562	17,423	18,085

¹SNPs identified at positions where there were SNPs within channel catfish; ²SNPs identified at positions where there were SNPs within blue catfish; ³SNPs identified at positions where there were no intra-specific channel catfish SNPs or intra-specific blue catfish SNPs, but the bases differed between the two species.

ISSN: 1471-2164