| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3612 | 41712 | T | G | 24 | 681.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3612 | 41896 | A | T | 16 | 351.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3612 | 42100 | A | C | 18 | 169.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3617 | 7541 | G | C | 250 | 181.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3620 | 14754 | T | G | 229 | 81.77 | noncoding | Transversion | 0/1 | NAD(P)H-quinone oxidoreductase subunit 2 B, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase, subunit 2 B) (NADH-plastoquinone oxidoreductase subunit 2 B) |
| Scaffold_3622 | 4681 | T | G | 20 | 46.77 | 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_3622 | 5300 | C | G | 29 | 195.77 | 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_3625 | 26127 | T | G | 10 | 322.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3626 | 59491 | A | T | 10 | 151.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3632 | 133 | T | G | 59 | 2214.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3633 | 35345 | C | A | 11 | 333.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3633 | 35438 | A | C | 15 | 49.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3634 | 25091 | G | T | 50 | 745.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3635 | 17916 | C | A | 54 | 1498.77 | CDS | Transversion | 1/1 | CLIP-associated protein (AtCLASP) |
| Scaffold_3641 | 30929 | G | T | 49 | 1876.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3642 | 20073 | A | C | 13 | 101.77 | CDS | Transversion | 0/1 | Protein Ycf2 |
| Scaffold_3642 | 20222 | T | G | 86 | 2966.77 | exon | Transversion | 1/1 | Protein Ycf2 |
| Scaffold_3650 | 49299 | C | A | 196 | 1449.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3400 | A | C | 34 | 932.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3651 | 3446 | G | T | 59 | 1114.77 | noncoding | Transversion | 0/1 | Unannotated |