Table 2 Number of putative and validated SNPs from each dataset
SNP Group | Total SNPs | Polymorphic | Monomorphic | Failed assay | Success rate |
|---|---|---|---|---|---|
All putative SNPs (95,234) | 92 | 72 | 11 | 9 | 86.7% |
GATK/SAMTool common SNPs (50,289) | 88 | 72 | 8 | 8 | 90.0% |
Total SNPs with allelic imbalance | 68 | 55 | 7 | 6 | 88.7% |
GATK unique SNPs with allelic imbalance | 25 | 21 | 3 | 1 | 87.5% |
SAMTool unique SNPs with allelic imbalance | 10 | 4 | 2 | 4 | 66.7% |
GATK/SAMTool common SNPs with allelic imbalance | 33 | 30 | 2 | 1 | 93.8% |