| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3353 | 22280 | A | G | 16 | 470.96 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3358 | 4180 | G | A | 40 | 50.77 | exon | Transition | 0/1 | COMPASS-like H3K4 histone methylase component WDR5A (AtWDR5A) |
| Scaffold_3360 | 41443 | T | C | 239 | 742.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3360 | 41444 | C | T | 241 | 117.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3360 | 41682 | G | A | 24 | 603.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3360 | 63622 | A | G | 250 | 632.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3360 | 63635 | A | G | 248 | 1006.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3361 | 26476 | A | G | 19 | 49.77 | noncoding | Transition | 0/1 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) |
| Scaffold_3362 | 2810 | T | C | 32 | 1065.77 | intron | Transition | 1/1 | Unannotated |
| Scaffold_3362 | 2857 | A | G | 250 | 286.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3362 | 3264 | A | G | 16 | 43.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3362 | 3411 | C | T | 33 | 136.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3362 | 3426 | A | G | 13 | 277.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3362 | 3937 | C | T | 250 | 714.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3362 | 3975 | C | T | 245 | 6821.77 | CDS | Transition | 1/1 | Unannotated |
| Scaffold_3365 | 7695 | A | G | 250 | 150.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3365 | 7697 | A | G | 249 | 322.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3365 | 7774 | T | C | 250 | 70.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3365 | 7775 | A | G | 249 | 404.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3368 | 1348 | C | T | 18 | 257.77 | CDS | Transition | 0/1 | Unannotated |