Table 1

Summary of SNP detection approach
SNP detection AA6 AM20 AA3 AM22
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%

Wong et al.

Wong et al. BMC Genomics 2012 13:726   doi:10.1186/1471-2164-13-726

Open Data