| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3116 | 6886 | C | T | 12 | 110.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3116 | 6898 | T | C | 12 | 107.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3121 | 21359 | T | C | 20 | 300.77 | noncoding | Transition | 0/1 | Protein ABCI12, chloroplastic (ABC transporter I family member 12) (ABC transporter ABCI.12) (AtABCI12) |
| Scaffold_3122 | 41263 | G | A | 11 | 46.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3124 | 58264 | C | T | 13 | 32.77 | intron | Transition | 0/1 | O-fucosyltransferase 39 (O-FucT-39) (EC 2.4.1.-) (O-fucosyltransferase family protein) |
| Scaffold_3124 | 58310 | A | G | 80 | 2137.77 | CDS | Transition | 0/1 | O-fucosyltransferase 39 (O-FucT-39) (EC 2.4.1.-) (O-fucosyltransferase family protein) |
| Scaffold_3125 | 9392 | T | C | 10 | 131.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3125 | 9417 | G | A | 15 | 255.84 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3125 | 9484 | G | A | 23 | 491.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3125 | 9677 | C | T | 23 | 546.78 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 121 | C | T | 250 | 95.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 124 | T | C | 250 | 842.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 168 | A | G | 250 | 5262.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 176 | A | G | 249 | 4821.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 299 | G | A | 250 | 2537.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 412 | T | C | 250 | 230.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 503 | C | T | 250 | 1671.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 566 | C | T | 250 | 1456.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 730 | T | C | 250 | 3579.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3128 | 766 | G | A | 250 | 3366.77 | exon | Transition | 0/1 | Unannotated |