| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3824 | 10845 | T | G | 250 | 71.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3824 | 17309 | G | C | 144 | 49.74 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3832 | 26526 | G | T | 214 | 3230.05 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3832 | 26530 | G | T | 104 | 3712.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3835 | 1822 | A | T | 18 | 274.77 | 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_3841 | 45858 | G | C | 24 | 851.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3845 | 1546 | G | C | 62 | 1558.78 | exon | Transversion | 1/1 | Stem-specific protein TSJT1 |
| Scaffold_3846 | 19631 | T | G | 11 | 32.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3848 | 6856 | T | G | 48 | 1377.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3850 | 19376 | T | A | 29 | 275.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3853 | 13205 | C | G | 139 | 4896.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3853 | 13206 | T | G | 135 | 4617.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3854 | 39614 | A | T | 249 | 176.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3854 | 40364 | A | T | 249 | 162.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3855 | 30179 | T | A | 38 | 1365.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3856 | 80466 | A | T | 250 | 172.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3856 | 80885 | A | C | 250 | 1107.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3856 | 80886 | A | T | 250 | 845.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3858 | 104 | T | A | 78 | 204.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3859 | 40163 | A | C | 36 | 1238.77 | noncoding | Transversion | 1/1 | Unannotated |