Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

Table 7 Estimation of proportions of inter-specific and intra-specific SNPs from the set of filtered SNPs identified from the interspecific all catfish EST assembly

SNP type*	From 1,000 random contigs	Estimated from the all catfish assembly	Estimated % of total filtered SNP
Inter-specific SNP¹	430	18,731	39
Intra-specific SNP, blue catfish²	12	523	1
Intra-specific SNP, channel catfish³	54	2,352	5
Intra-specific SNP, blue catfish and channel catfish⁴	87	3,790	8
Undetermined⁵	383	16,683	34
Subtotal	966	42,080	87
SNP from only blue catfish ESTs⁶	NA	1,118	2
SNP from only channel catfish ESTs⁶	NA	5,396	11
Subtotal	NA	6,514	13
Total SNP	NA	48,594	100

*SNPs were identified from contigs containing at least four sequences with at least two sequences from either channel catfish or blue catfish in the all catfish EST assembly: ¹where there were no intra-specific blue catfish SNPs or intra-specific channel catfish SNPs, but the sequence differed between the two species at the inter-specific SNP position; ²where there were SNPs within blue catfish, but not within channel catfish; ³where there were SNPs within channel catfish, but not within blue catfish; ⁴where there were SNPs within both blue catfish and channel catfish; ⁵undetermined because overall the SNPs qualified as SNPs with at least two minor allele sequences, but only one of the minor allele sequences was from one of the two species of blue catfish or channel catfish; ⁶these SNPs were identified from ESTs that have been sequenced from only one of the two species, blue catfish or channel catfish, to date.

ISSN: 1474-760X