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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

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

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
  1. *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.