| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3789 | 22629 | G | T | 26 | 60.77 | 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_3791 | 8607 | A | T | 248 | 816.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3791 | 8618 | A | T | 249 | 67.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3797 | 27098 | A | C | 14 | 205.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3798 | 6135 | A | C | 44 | 1067.77 | CDS | Transversion | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 6181 | A | T | 46 | 94.77 | CDS | Transversion | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 6219 | A | T | 26 | 616.77 | CDS | Transversion | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 6321 | A | C | 24 | 246.77 | CDS | Transversion | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3798 | 6397 | C | G | 15 | 140.77 | intron | Transversion | 0/1 | 12-oxophytodienoate reductase 3 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 3) (OPDA-reductase 3) (LeOPR3) |
| Scaffold_3801 | 725 | T | A | 11 | 30.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3801 | 8058 | G | T | 249 | 43.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3803 | 20606 | T | A | 80 | 80.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3803 | 20645 | G | C | 81 | 614.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3803 | 20686 | T | A | 33 | 269.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3806 | 3894 | G | T | 15 | 30.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3806 | 44115 | T | G | 250 | 8549.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3806 | 44286 | A | C | 14 | 138.79 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3810 | 783 | G | C | 64 | 430.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3810 | 847 | A | T | 23 | 379.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3813 | 54226 | C | G | 114 | 4233.77 | noncoding | Transversion | 1/1 | Protein TIC 214 (Translocon at the inner envelope membrane of chloroplasts 214) (AtTIC214) |