| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3462 | 19327 | T | C | 12 | 43.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3466 | 13977 | A | G | 15 | 266.1 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 17540 | A | G | 85 | 154.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 17579 | C | T | 91 | 118.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 17780 | T | C | 61 | 1483.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 17786 | A | G | 53 | 1204.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 17807 | A | G | 17 | 83.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 57732 | T | C | 26 | 198.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 59422 | A | G | 28 | 556.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 59466 | C | T | 71 | 911.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3472 | 59491 | C | T | 86 | 1470.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3476 | 55137 | C | T | 10 | 153.77 | noncoding | Transition | 0/1 | 30S ribosomal protein S16, chloroplastic |
| Scaffold_3477 | 26718 | G | A | 11 | 218.84 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3477 | 61612 | G | A | 10 | 92.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3477 | 62403 | G | A | 250 | 4231.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3477 | 62553 | G | A | 33 | 838.81 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3479 | 16087 | C | T | 10 | 222.84 | noncoding | Transition | 0/1 | ATP synthase subunit alpha, mitochondrial |
| Scaffold_3480 | 40547 | A | G | 246 | 320.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3480 | 40559 | G | A | 246 | 1408.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3480 | 40721 | A | G | 250 | 226.77 | exon | Transition | 0/1 | Unannotated |