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Table 5 Summary of SNP identification from the catfish ESTs

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

  Number of SNPs
SNP Blue catfish Channel catfish All catfish
Putative    
   Transitions 29,305 61,184 172,746
   Transversions 19,397 41,068 130,254
   Total SNPs 48,702 102,252 303,000
   Indels 14,803 41,660 100,636
   SNP rate (kb) 3.2 4.1 7.7
Filtered putative    
   Transitions 2,886 11,012 32,235
   Transversions 1,005 4,815 16,359
   Total SNPs 3,891 15,827 48,594
   Indels 1,070 6,707 19,398
   Filtered/Non-filtered rate 7.8% 15.7% 16.2%
   SNP rate* (kb) 0.25 0.64 1.6
  1. *SNP rate was calculated by dividing the total number of SNPs excluding indels by the total length (bp) of the consensus sequences of the contigs.