| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3633 | 35428 | T | C | 12 | 249.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3633 | 35429 | T | C | 12 | 252.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3637 | 6061 | C | T | 250 | 8057.77 | noncoding | Transition | 1/1 | NAD(P)H-quinone oxidoreductase subunit H, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase subunit H) (NADH-plastoquinone oxidoreductase 49 kDa subunit) (NADH-plastoquinone oxidoreductase subunit H) |
| Scaffold_3639 | 6 | C | T | 20 | 39.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase, subunit 2 A) (NADH-plastoquinone oxidoreductase subunit 2 A) |
| Scaffold_3639 | 157 | C | T | 249 | 1813.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase, subunit 2 A) (NADH-plastoquinone oxidoreductase subunit 2 A) |
| Scaffold_3639 | 166 | C | T | 250 | 272.77 | noncoding | Transition | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 A, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase, subunit 2 A) (NADH-plastoquinone oxidoreductase subunit 2 A) |
| Scaffold_3639 | 364 | G | A | 52 | 61.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3639 | 12806 | C | T | 10 | 30.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3639 | 12807 | T | C | 10 | 30.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3642 | 20221 | A | G | 49 | 1417.77 | exon | Transition | 1/1 | Protein Ycf2 |
| Scaffold_3643 | 28336 | C | T | 45 | 383.77 | noncoding | Transition | 0/1 | Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta, chloroplastic (ACCase subunit beta) (Acetyl-CoA carboxylase carboxyltransferase subunit beta) (EC 2.1.3.15) |
| Scaffold_3645 | 34883 | G | A | 16 | 138.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3651 | 3486 | C | T | 39 | 64.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3652 | 60262 | T | C | 250 | 991.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3653 | 22332 | A | G | 89 | 3053.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3653 | 22335 | T | C | 238 | 6950.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3657 | 16165 | G | A | 41 | 42.79 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3660 | 15881 | C | T | 15 | 243.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3660 | 19707 | A | G | 250 | 75.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3660 | 19925 | C | T | 25 | 149.77 | intron | Transition | 0/1 | Unannotated |