| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3480 | 40646 | T | G | 250 | 5201.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40683 | A | T | 247 | 120.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40716 | G | C | 247 | 3027.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40770 | T | A | 86 | 1256.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3481 | 28544 | G | T | 15 | 93.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3487 | 4921 | T | A | 14 | 64.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3487 | 17443 | C | A | 17 | 75.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3487 | 22210 | G | T | 10 | 45.77 | noncoding | 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_3488 | 37520 | T | G | 30 | 531.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3491 | 20016 | T | G | 11 | 92.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3492 | 5946 | A | T | 59 | 233.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3497 | 41047 | T | G | 16 | 276.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3498 | 22374 | T | G | 28 | 407.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3503 | 27979 | G | C | 249 | 185.77 | noncoding | Transversion | 0/1 | ATP synthase subunit b, chloroplastic (ATP synthase F(0) sector subunit b) (ATPase subunit I) |
| Scaffold_3506 | 23381 | A | T | 87 | 34.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3507 | 68615 | A | C | 81 | 2925.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3507 | 68622 | C | G | 69 | 2383.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3508 | 17285 | C | A | 102 | 47.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3508 | 17286 | C | G | 95 | 90.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3512 | 33526 | G | C | 233 | 47.77 | noncoding | Transversion | 0/1 | Unannotated |