| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_45 | 388134 | A | G | 109 | 1631.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_45 | 388217 | G | A | 145 | 2371.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_45 | 388382 | T | C | 82 | 1187.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_45 | 388424 | A | G | 55 | 824.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_45 | 388523 | C | T | 65 | 44.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_45 | 514069 | C | T | 16 | 298.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_45 | 680853 | G | A | 10 | 106.77 | intron | Transition | 0/1 | Glutamyl-tRNA reductase 2, chloroplastic (GluTR) (EC 1.2.1.70) |
| Scaffold_45 | 969827 | C | T | 15 | 31.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_46 | 43886 | T | C | 13 | 132.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_46 | 72986 | G | A | 41 | 371.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_46 | 85324 | T | C | 32 | 194.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_46 | 85567 | G | A | 16 | 348.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_46 | 97125 | T | C | 12 | 46.77 | CDS | Transition | 0/1 | Chromatin remodeling protein EBS (Protein EARLY BOLTING IN SHORT DAYS) |
| Scaffold_46 | 309113 | A | G | 13 | 63.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_46 | 514180 | C | T | 23 | 66.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_46 | 514297 | T | C | 12 | 148.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_46 | 545963 | A | G | 19 | 331.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_46 | 650467 | G | A | 11 | 106.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_46 | 665419 | C | T | 184 | 455.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_46 | 1258607 | A | G | 128 | 2248.77 | CDS | Transition | 0/1 | Cytochrome P450 81E8 (EC 1.14.13.-) |