Table 1 Summary of SNP detection approach

BWA

1) Percentage of mapped reads

11.92%

11.31%

15.84%

11.57%

2) Putative SNPs

8,345

4,652

3,885

972

Bowtie

1) Percentage of mapped reads

22.57%

21.15%

39.71%

22.21%

2) Putative SNPs

18,684

11,093

10,993

2,516

3) Number of SNPs after Filter 1

11,439

5,738

6,711

861

4) Number of SNPs after Filter 2

6,199

3,179

4,508

629

5) Number of SNPs after Filter 2 with design score >; 0.4

5,094

2,210

3,996

438

6) Validation rate of SNPs after Filter 2

50%

50%

20%

26.7%