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.

Wang et al. Genome Biology 2010 11:R8   doi:10.1186/gb-2010-11-1-r8

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