| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3010 | 49756 | A | G | 250 | 245.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3010 | 49764 | T | C | 249 | 305.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3015 | 8730 | T | C | 11 | 58.77 | exon | Transition | 0/1 | UDP-glycosyltransferase 87A1 (EC 2.4.1.-) |
| Scaffold_3022 | 22079 | A | G | 10 | 45.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3022 | 42366 | A | G | 250 | 369.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3025 | 5275 | C | T | 18 | 117.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3025 | 45725 | A | G | 24 | 138.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45741 | G | A | 19 | 331.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45833 | C | T | 30 | 31.77 | noncoding | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3025 | 45854 | G | A | 21 | 523.96 | noncoding | Transition | 1/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3026 | 10328 | G | A | 12 | 129.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 4115 | T | C | 88 | 190.77 | noncoding | Transition | 0/1 | Protein TIC 214 (Translocon at the inner envelope membrane of chloroplasts 214) (AtTIC214) |
| Scaffold_3027 | 49221 | G | A | 250 | 558.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52135 | T | C | 22 | 455.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52185 | G | A | 15 | 304.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52216 | C | T | 10 | 120.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52314 | T | C | 17 | 95.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52322 | C | T | 15 | 100.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 52500 | T | C | 11 | 112.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3027 | 57570 | T | C | 19 | 117.77 | noncoding | Transition | 0/1 | Cytochrome b6-f complex subunit 4 (17 kDa polypeptide) |