| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3954 | 35901 | G | C | 68 | 53.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 35980 | T | A | 30 | 37.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 43494 | T | G | 207 | 7500.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3954 | 65278 | C | G | 12 | 242.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 65340 | T | A | 18 | 479.89 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_3957 | 14299 | C | A | 20 | 534.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3961 | 56305 | T | G | 250 | 96.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3961 | 56317 | G | T | 250 | 759.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3961 | 56332 | C | G | 250 | 416.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3962 | 28263 | T | A | 13 | 60.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 28510 | T | A | 27 | 196.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 28750 | A | T | 34 | 326.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 28758 | A | T | 40 | 423.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 28816 | T | A | 25 | 80.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 28978 | C | A | 10 | 61.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3962 | 29254 | G | T | 47 | 446.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog |
| Scaffold_3968 | 30255 | C | G | 27 | 268.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3969 | 44864 | T | G | 69 | 1661.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3969 | 45054 | A | T | 11 | 58.77 | exon | Transversion | 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_3969 | 45158 | A | T | 48 | 811.77 | exon | Transversion | 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] |