| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2485 | 122642 | G | C | 10 | 266.8 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2486 | 52335 | G | T | 146 | 1765.77 | intron | Transversion | 0/1 | Mitogen-activated protein kinase 3 (AtMPK3) (MAP kinase 3) (EC 2.7.11.24) |
| Scaffold_2488 | 4963 | C | A | 10 | 54.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2490 | 50332 | A | T | 14 | 169.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2493 | 49601 | T | A | 17 | 43.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2495 | 103712 | G | C | 42 | 55.77 | exon | Transversion | 0/1 | U-box domain-containing protein 30 (EC 2.3.2.27) (Plant U-box protein 30) (RING-type E3 ubiquitin transferase PUB30) |
| Scaffold_2495 | 104062 | T | G | 18 | 80.77 | exon | Transversion | 0/1 | U-box domain-containing protein 30 (EC 2.3.2.27) (Plant U-box protein 30) (RING-type E3 ubiquitin transferase PUB30) |
| Scaffold_2495 | 104347 | A | C | 12 | 67.77 | exon | Transversion | 0/1 | U-box domain-containing protein 30 (EC 2.3.2.27) (Plant U-box protein 30) (RING-type E3 ubiquitin transferase PUB30) |
| Scaffold_2495 | 104567 | T | G | 27 | 88.77 | exon | Transversion | 0/1 | U-box domain-containing protein 30 (EC 2.3.2.27) (Plant U-box protein 30) (RING-type E3 ubiquitin transferase PUB30) |
| Scaffold_2495 | 104837 | T | G | 15 | 191.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2495 | 104899 | G | T | 13 | 205.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2495 | 104921 | C | G | 11 | 182.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2496 | 11758 | G | T | 39 | 272.77 | CDS | Transversion | 0/1 | Ubiquitin receptor RAD23c (AtRAD23c) (Putative DNA repair protein RAD23-3) (RAD23-like protein 3) (AtRAD23-3) |
| Scaffold_2497 | 110559 | C | A | 12 | 340.78 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2498 | 57334 | T | A | 13 | 354.78 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2501 | 35406 | C | A | 11 | 237.84 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2502 | 46000 | T | G | 11 | 89.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2502 | 46001 | A | C | 18 | 337.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2502 | 46379 | A | C | 78 | 2600.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2504 | 69831 | T | A | 11 | 52.77 | intron | Transversion | 0/1 | Unannotated |