| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2475 | 122038 | T | C | 250 | 229.77 | CDS | Transition | 0/1 | Elongation factor 1-alpha (EF-1-alpha) |
| Scaffold_2475 | 125281 | A | G | 250 | 6594.77 | CDS | Transition | 0/1 | Hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase) (EC 2.3.3.10) (3-hydroxy-3-methylglutaryl coenzyme A synthase) (Protein EMBRYO DEFECTIVE 2778) (Protein FLAKY POLLEN 1) |
| Scaffold_2479 | 2429 | G | A | 15 | 89.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2479 | 118274 | A | G | 17 | 180.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2479 | 120303 | G | A | 35 | 163.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2480 | 25266 | T | C | 22 | 164.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2480 | 25267 | T | C | 22 | 192.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2480 | 115588 | C | T | 12 | 221.77 | exon | Transition | 0/1 | Organ-specific protein P4 |
| Scaffold_2482 | 26243 | A | G | 21 | 241.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2482 | 27069 | T | C | 39 | 56.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2482 | 91787 | C | T | 40 | 403.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2482 | 92731 | T | C | 112 | 2732.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2485 | 108704 | T | C | 19 | 43.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2486 | 81125 | T | C | 57 | 344.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2487 | 23395 | G | A | 78 | 267.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2487 | 99536 | T | C | 40 | 206.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2490 | 1005 | A | G | 59 | 822.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2490 | 1057 | A | G | 118 | 2478.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2490 | 1097 | G | A | 121 | 2154.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2490 | 1444 | C | T | 89 | 734.77 | noncoding | Transition | 0/1 | Unannotated |