Table 5

Summary of SNP identification from the catfish ESTs

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


*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.

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

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