| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_47 | 1700248 | T | C | 38 | 35.77 | exon | Transition | 0/1 | E3 ubiquitin-protein ligase PRT6 (EC 2.3.2.27) (Protein GREENING AFTER EXTENDED DARKNESS 1) (Protein PROTEOLYSIS 6) (RING-type E3 ubiquitin transferase PRT6) |
| Scaffold_47 | 1720477 | G | A | 47 | 620.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_47 | 1720597 | A | G | 248 | 3189.78 | exon | Transition | 0/1 | Unannotated |
| Scaffold_47 | 1757517 | A | G | 11 | 294.9 | intron | Transition | 0/1 | Unannotated |
| Scaffold_47 | 1757527 | T | C | 24 | 637.28 | intron | Transition | 1/1 | Unannotated |
| Scaffold_47 | 1852209 | A | G | 11 | 55.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 231032 | C | T | 43 | 464.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 231260 | T | C | 45 | 181.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 231263 | T | C | 46 | 180.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 231296 | T | C | 65 | 1240.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 231716 | A | G | 54 | 564.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 288689 | G | A | 26 | 39.77 | intron | Transition | 0/1 | 50S ribosomal protein L3, chloroplastic (Chloroplastic large ribosomal subunit protein uL3c) |
| Scaffold_48 | 326713 | C | T | 11 | 135.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_48 | 386018 | A | G | 10 | 252.84 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 386153 | G | A | 13 | 323.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 386180 | A | G | 18 | 476.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 557202 | G | A | 12 | 271.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_48 | 738810 | T | C | 25 | 94.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_48 | 899700 | G | A | 17 | 58.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_48 | 899701 | A | G | 17 | 58.77 | exon | Transition | 0/1 | Unannotated |