| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_368 | 5062 | G | T | 57 | 1012.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_368 | 5351 | A | C | 19 | 135.77 | intron | Transversion | 0/1 | Phosphoribulokinase, chloroplastic (PRK) (PRKase) (EC 2.7.1.19) (Phosphopentokinase) |
| Scaffold_375 | 21149 | C | A | 12 | 60.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_375 | 21165 | G | C | 12 | 53.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_378 | 15833 | C | G | 43 | 1076.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_380 | 56374 | T | A | 13 | 205.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_382 | 52581 | G | C | 13 | 115.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_384 | 2713 | C | A | 43 | 182.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_385 | 71736 | C | G | 36 | 68.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_386 | 76711 | G | C | 17 | 348.77 | noncoding | Transversion | 0/1 | Probable inactive shikimate kinase like 2, chloroplastic (AtSKL2) |
| Scaffold_391 | 21300 | C | A | 159 | 1146.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_392 | 36658 | A | T | 20 | 163.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_398 | 9414 | G | T | 49 | 151.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_400 | 43042 | G | T | 17 | 281.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_400 | 63974 | C | G | 11 | 247.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_400 | 64124 | G | T | 22 | 99.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_401 | 15310 | T | G | 72 | 79.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_402 | 34697 | A | C | 27 | 170.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_402 | 34698 | G | T | 30 | 401.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_404 | 64506 | T | G | 18 | 168.77 | intron | Transversion | 0/1 | Unannotated |