| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3236 | 35205 | G | A | 18 | 246.77 | CDS | Transition | 0/1 | Cellulose synthase-like protein D3 (AtCslD3) (EC 2.4.1.-) (Protein KOJAK) |
| Scaffold_3236 | 42821 | C | A,T | 32 | 989.77 | noncoding | Transition | 1/2 | Unannotated |
| Scaffold_3240 | 43592 | A | G | 11 | 63.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3240 | 43601 | G | A | 11 | 67.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3243 | 22376 | T | C | 14 | 341.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3243 | 73691 | A | G | 16 | 482.96 | exon | Transition | 1/1 | Mediator of RNA polymerase II transcription subunit 13 (Protein GRAND CENTRAL) (Protein MACCHI-BOU 2) |
| Scaffold_3244 | 18167 | T | C | 250 | 60.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18180 | T | C | 250 | 1105.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18185 | A | G | 250 | 74.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18186 | T | C | 249 | 1615.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18192 | T | C | 250 | 120.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18205 | T | C | 250 | 1664.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18222 | T | C | 250 | 775.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18233 | T | C | 250 | 1785.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18239 | T | C | 250 | 461.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18243 | T | C | 250 | 866.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18244 | T | C | 250 | 404.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3244 | 18345 | T | C | 59 | 1528.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3244 | 18348 | A | G | 22 | 598.81 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3248 | 34870 | C | T | 250 | 4772.77 | CDS | Transition | 0/1 | Unannotated |