| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3969 | 46167 | T | G | 21 | 327.77 | CDS | 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_3971 | 25105 | G | C | 250 | 466.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3971 | 25186 | A | T | 249 | 92.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3980 | 41433 | C | G | 23 | 34.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3980 | 51236 | A | T | 10 | 127.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3982 | 26300 | G | T | 247 | 39.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3987 | 20662 | A | C | 247 | 5013.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3987 | 20663 | G | T | 246 | 8892.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3987 | 20706 | A | C | 250 | 1556.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3994 | 12860 | T | A | 15 | 138.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3998 | 26458 | T | G | 127 | 4294.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_4004 | 15382 | T | A | 17 | 234.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_4004 | 15383 | T | G | 16 | 243.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_4005 | 48326 | A | C | 248 | 53.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_4005 | 48327 | A | C | 250 | 178.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_4005 | 56361 | C | A | 151 | 5194.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_4006 | 35056 | C | A | 10 | 30.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_4007 | 14838 | C | G | 103 | 3433.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_4007 | 14839 | C | A | 93 | 3417.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_4007 | 31543 | A | C | 250 | 5101.77 | noncoding | Transversion | 0/1 | Unannotated |