| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3172 | 16641 | C | T | 12 | 116.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3177 | 43325 | C | T | 54 | 1490.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3177 | 43339 | C | T | 52 | 1203.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3177 | 43387 | C | T | 13 | 259.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3177 | 63658 | C | T | 17 | 49.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3177 | 63998 | T | C | 11 | 35.77 | intron | Transition | 0/1 | Uncharacterized mitochondrial protein AtMg01060 (ORF107g) |
| Scaffold_3177 | 64015 | C | T | 12 | 61.77 | CDS | Transition | 0/1 | Uncharacterized mitochondrial protein AtMg01060 (ORF107g) |
| Scaffold_3179 | 54120 | C | T | 249 | 5458.77 | noncoding | Transition | 1/1 | Cytochrome b559 subunit alpha (PSII reaction center subunit V) |
| Scaffold_3179 | 54186 | C | T | 34 | 777.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3180 | 32901 | C | T | 250 | 1464.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3180 | 33482 | G | A | 246 | 8571.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3183 | 16454 | G | A | 56 | 187.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3183 | 16877 | G | A | 37 | 56.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3183 | 16973 | G | A | 35 | 64.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3183 | 17055 | T | C | 40 | 32.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3183 | 17151 | G | A | 89 | 75.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3185 | 748 | G | A | 15 | 251.8 | exon | Transition | 1/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_3185 | 756 | G | A | 15 | 245.8 | exon | Transition | 1/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_3192 | 6 | A | G | 247 | 135.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3192 | 10 | A | G | 250 | 56.77 | noncoding | Transition | 0/1 | Unannotated |