Table 4.
Overlapped and uniques SNPs called using two different calling methods (GATK and in-house script) from mapping using E. grandis reference genome.
| Species | Methods | filtered SNP counts | % unique SNP positions | % shared SNP positions between GATK and inhouse script methods |
|---|---|---|---|---|
| A. gummiferum | GATK (Haplotype Caller) | 142,294 | 66 | 34 |
| Inhouse script | 73,765 | 34 | 66 | |
| S. longifolium | GATK (Haplotype Caller) | 181,967 | 79 | 21 |
| Inhouse script | 68,106 | 45 | 55 | |
| T. glauca-BDS | GATK (Haplotype Caller) | 148,484 | 75 | 25 |
| Inhouse script | 67,115 | 44 | 56 | |
| T. glauca-FAR | GATK (Haplotype Caller) | 137,073 | 60 | 40 |
| Inhouse script | 83,243 | 34 | 66 |