| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3929 | 37009 | A | C | 17 | 49.74 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3929 | 48719 | C | G | 88 | 657.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3929 | 48720 | A | C | 250 | 7422.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3929 | 48724 | A | T | 250 | 282.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3933 | 30962 | G | C | 239 | 195.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3933 | 30970 | C | A | 56 | 42.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 11926 | A | C | 174 | 5013.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3934 | 12221 | T | A | 13 | 205.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 12235 | C | G | 27 | 699.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 12354 | C | A | 10 | 76.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 12824 | A | T | 42 | 859.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 12861 | G | C | 37 | 683.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 41852 | C | A | 10 | 33.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3934 | 41853 | C | G | 10 | 30.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3942 | 33761 | C | A | 17 | 246.77 | CDS | 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_3948 | 6473 | C | G | 64 | 188.77 | exon | Transversion | 0/1 | Protein transport protein SEC16A homolog (Protein MAIGO 5) |
| Scaffold_3948 | 6535 | A | T | 11 | 61.77 | exon | Transversion | 0/1 | Protein transport protein SEC16A homolog (Protein MAIGO 5) |
| Scaffold_3948 | 6541 | C | A | 14 | 149.77 | exon | Transversion | 0/1 | Protein transport protein SEC16A homolog (Protein MAIGO 5) |
| Scaffold_3949 | 9325 | T | G | 32 | 84.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3949 | 9750 | A | C | 13 | 55.77 | CDS | Transversion | 0/1 | Unannotated |