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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.
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Genome Biology

ISSN: 1474-760X

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