| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_40 | 40519 | T | C | 10 | 169.78 | intron | Transition | 0/1 | Unannotated |
| Scaffold_40 | 97808 | A | G | 11 | 39.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_40 | 140870 | T | C | 10 | 61.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 140874 | C | T | 18 | 111.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 317121 | A | G | 17 | 74.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 345102 | A | G | 20 | 40.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 505489 | T | C | 11 | 36.77 | noncoding | Transition | 0/1 | Putative 1-phosphatidylinositol-3-phosphate 5-kinase FAB1D (Phosphatidylinositol 3-phosphate 5-kinase) (EC 2.7.1.150) (Phosphatidylinositol 3-phosphate 5-kinase type III) (PIPkin-III) (Type III PIP kinase) (Protein FORMS APLOID AND BINUCLEATE CELLS 1D) |
| Scaffold_40 | 513485 | C | T | 31 | 490.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_40 | 613408 | C | T | 16 | 46.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_40 | 638035 | T | C | 19 | 37.77 | exon | Transition | 0/1 | Scarecrow-like protein 13 (AtSCL13) (GRAS family protein 24) (AtGRAS-24) |
| Scaffold_40 | 681099 | G | A | 10 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 692859 | A | G | 38 | 54.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 807894 | A | G | 15 | 55.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_40 | 923106 | G | A | 10 | 81.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_40 | 923135 | G | A | 10 | 30.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_40 | 1163227 | G | A | 12 | 58.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_40 | 1163228 | G | A | 12 | 55.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_40 | 1167436 | C | T | 25 | 31.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_40 | 1167437 | T | C | 25 | 31.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_40 | 1267211 | T | C | 27 | 259.77 | noncoding | Transition | 0/1 | Unannotated |