| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2685 | 129634 | A | G | 139 | 1976.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2685 | 129775 | A | G | 184 | 370.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2685 | 189696 | G | A | 27 | 48.77 | exon | Transition | 0/1 | SEC1 family transport protein SLY1 (AtSLY1) |
| Scaffold_2686 | 87908 | A | G | 18 | 68.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2688 | 39307 | T | C | 50 | 49.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2690 | 49921 | A | G | 31 | 106.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2690 | 132757 | T | C | 20 | 34.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2692 | 136045 | T | C | 14 | 92.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2693 | 32001 | C | T | 25 | 40.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2693 | 147396 | C | T | 13 | 121.77 | exon | Transition | 0/1 | Probable glucan endo-1,3-beta-glucosidase A6 (EC 3.2.1.39) ((1->3)-beta-glucan endohydrolase) ((1->3)-beta-glucanase) (Anther-specific protein A6) (Beta-1,3-endoglucanase) (Protein MATERNAL EFFECT EMBRYO ARREST 48) |
| Scaffold_2694 | 22738 | C | T | 32 | 33.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2694 | 132754 | A | G | 12 | 146.03 | exon | Transition | 1/1 | Unannotated |
| Scaffold_2695 | 158330 | T | C | 123 | 32.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_2695 | 243286 | T | C | 18 | 40.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2695 | 243970 | C | T | 22 | 52.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2695 | 244395 | C | T | 12 | 64.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_2696 | 20795 | G | A | 10 | 38.77 | intron | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE1 (Retro element 1) (AtRE1) [Includes: Protease RE1 (EC 3.4.23.-); Reverse transcriptase RE1 (EC 2.7.7.49); Endonuclease RE1] |
| Scaffold_2696 | 20816 | C | T | 12 | 32.77 | intron | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE1 (Retro element 1) (AtRE1) [Includes: Protease RE1 (EC 3.4.23.-); Reverse transcriptase RE1 (EC 2.7.7.49); Endonuclease RE1] |
| Scaffold_2696 | 21734 | C | T | 16 | 97.77 | noncoding | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_2696 | 53138 | G | A | 37 | 124.77 | CDS | Transition | 0/1 | Unannotated |