| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_46 | 1107256 | A | C | 13 | 115.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1153009 | A | T | 11 | 306.56 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1258925 | G | T | 13 | 143.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1262632 | T | A | 25 | 557.56 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1263030 | A | C | 26 | 220.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1635757 | C | A | 239 | 539.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_46 | 1897181 | A | C | 11 | 49.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 191657 | T | A | 10 | 158.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 212129 | T | G | 56 | 200.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 244186 | T | A | 250 | 4273.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 244189 | A | T | 250 | 3525.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 248683 | G | C | 72 | 920.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 250506 | T | G | 250 | 5130.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 303458 | A | C | 14 | 49.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 367892 | G | T | 20 | 88.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 413079 | G | C | 100 | 2079.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 447936 | A | T | 18 | 32.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 447937 | G | T | 15 | 215.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_47 | 972904 | C | A | 76 | 127.77 | CDS | Transversion | 0/1 | Probable carotenoid cleavage dioxygenase 4, chloroplastic (AtCCD4) (EC 1.14.99.-) (AtNCED4) |
| Scaffold_47 | 1150684 | T | G | 178 | 439.77 | CDS | Transversion | 0/1 | Elongation factor 2 (EF-2) (Protein LOW EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1) |