| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3166 | 51209 | A | C | 21 | 485.53 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3166 | 52161 | A | T | 38 | 824.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3167 | 45893 | T | G | 15 | 52.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3170 | 49669 | G | T | 13 | 39.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3171 | 51640 | T | A | 18 | 31.77 | CDS | Transversion | 0/1 | Beta-galactosidase 3 (Lactase 3) (EC 3.2.1.23) |
| Scaffold_3174 | 36056 | G | T | 55 | 52.74 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3174 | 36057 | G | C | 64 | 52.74 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3177 | 43224 | G | T | 36 | 1028.56 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3180 | 7337 | A | T | 249 | 395.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 7428 | T | G | 24 | 335.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 7429 | G | T | 17 | 50.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 32903 | A | C | 250 | 48.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 32907 | A | T | 246 | 379.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 33561 | A | T | 246 | 151.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 33771 | A | C | 249 | 153.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3185 | 306 | C | A | 10 | 138.77 | exon | Transversion | 0/1 | 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 | 64 | T | G | 250 | 395.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3192 | 66 | G | C | 250 | 194.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3192 | 76 | T | A | 249 | 501.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3192 | 182 | A | T | 246 | 78.77 | noncoding | Transversion | 0/1 | Unannotated |