| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3112 | 20880 | A | G | 250 | 326.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3113 | 46720 | G | A | 14 | 242.77 | exon | 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_3115 | 11236 | G | A | 12 | 121.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 11652 | A | G | 20 | 521.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 11687 | C | T | 31 | 632.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 11718 | C | T | 49 | 133.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 11916 | C | T | 19 | 95.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 12343 | T | C | 10 | 232.8 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 13037 | C | T | 39 | 122.77 | exon | Transition | 0/1 | RNA-directed DNA polymerase homolog (EC 2.7.7.48) (Reverse transcriptase homolog) |
| Scaffold_3115 | 13078 | A | G | 38 | 124.77 | exon | Transition | 0/1 | RNA-directed DNA polymerase homolog (EC 2.7.7.48) (Reverse transcriptase homolog) |
| Scaffold_3115 | 14425 | C | T | 14 | 110.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3115 | 22839 | A | G | 250 | 4673.77 | noncoding | Transition | 0/1 | Cytochrome b6 |
| Scaffold_3115 | 22846 | C | T | 250 | 975.77 | noncoding | Transition | 0/1 | Cytochrome b6 |
| Scaffold_3115 | 23056 | C | T | 10 | 83.77 | noncoding | Transition | 0/1 | Cytochrome b6 |
| Scaffold_3117 | 26324 | C | T | 101 | 78.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3117 | 28343 | C | T | 179 | 2569.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3117 | 28364 | C | T | 123 | 454.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3117 | 29012 | C | T | 200 | 3132.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3117 | 29087 | C | T | 249 | 3552.77 | CDS | Transition | 0/1 | Uncharacterized mitochondrial protein ymf40 (ORF502) |
| Scaffold_3117 | 29151 | C | T | 250 | 259.77 | CDS | Transition | 0/1 | Uncharacterized mitochondrial protein ymf40 (ORF502) |