| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3798 | 6411 | T | C | 17 | 442.79 | intron | Transition | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 6412 | A | G | 13 | 294.77 | intron | Transition | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 29415 | T | C | 13 | 147.77 | CDS | Transition | 0/1 | Probable sodium/metabolite cotransporter BASS4, chloroplastic (Bile acid transporter 4) (Bile acid-sodium symporter family protein 4) |
| Scaffold_3798 | 40760 | A | G | 41 | 547.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3798 | 42198 | T | C | 19 | 241.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3808 | 28388 | A | G | 14 | 271.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3810 | 54998 | T | C | 12 | 63.77 | intron | Transition | 0/1 | Uncharacterized protein At2g37660, chloroplastic |
| Scaffold_3811 | 57062 | T | C | 96 | 862.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 57137 | G | A | 111 | 354.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 57152 | T | C | 106 | 526.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 57233 | G | A | 135 | 320.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58035 | A | G | 57 | 40.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58044 | G | A | 55 | 45.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58084 | G | A | 33 | 748.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58158 | A | G | 10 | 279.22 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58344 | T | C | 28 | 154.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58365 | G | A | 12 | 232.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 58366 | C | T | 12 | 229.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3811 | 59158 | T | C | 60 | 932.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3822 | 1323 | C | T | 179 | 4067.77 | noncoding | Transition | 0/1 | Unannotated |