| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2637 | 958 | C | A | 12 | 69.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2637 | 31423 | A | T | 13 | 91.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2637 | 31441 | A | T | 13 | 110.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2639 | 42503 | A | C | 11 | 175.77 | intron | Transversion | 0/1 | Magnesium-chelatase subunit ChlD, chloroplastic (Mg-chelatase subunit D) (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase subunit ChlD) |
| Scaffold_2639 | 52763 | T | A | 16 | 146.77 | intron | Transversion | 0/1 | Calcium-dependent protein kinase 2 (CDPK 2) (EC 2.7.11.1) |
| Scaffold_2642 | 64466 | C | A | 11 | 403.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2642 | 64501 | G | C | 22 | 687.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2647 | 66117 | T | A | 10 | 293.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2648 | 41495 | A | T | 12 | 379.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2653 | 87346 | A | C | 23 | 789.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2667 | 59435 | T | A | 24 | 369.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2669 | 39386 | A | T | 58 | 1001.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2669 | 62691 | G | C | 12 | 58.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2669 | 80682 | T | A | 43 | 1382.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2672 | 39889 | C | A | 19 | 411.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2676 | 61859 | T | G | 47 | 1445.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2678 | 167927 | A | C | 18 | 74.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2680 | 83111 | C | A | 10 | 72.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2681 | 48008 | G | T | 11 | 289.9 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2681 | 55397 | T | G | 16 | 550.77 | intron | Transversion | 1/1 | Unannotated |