| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3789 | 22648 | A | T | 23 | 111.77 | CDS | Transversion | 0/1 | Uncharacterized mitochondrial protein AtMg00240 (ORF111a) |
| Scaffold_3791 | 8607 | A | T | 248 | 490.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3791 | 8618 | A | T | 250 | 471.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3791 | 31664 | C | A | 16 | 316.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3792 | 35053 | T | A | 100 | 3521.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3794 | 201 | G | T | 72 | 215.77 | CDS | Transversion | 0/1 | Reticulon-like protein B18 (AtRTNLB18) |
| Scaffold_3794 | 798 | G | C | 11 | 277.9 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3794 | 1295 | G | T | 26 | 459.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3794 | 30878 | A | C | 250 | 263.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3794 | 30987 | G | T | 40 | 1545.77 | noncoding | Transversion | 1/1 | Uncharacterized mitochondrial protein AtMg00860 (ORF158) |
| Scaffold_3797 | 27098 | A | C | 32 | 309.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3798 | 6135 | A | C | 18 | 325.77 | 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 | 20 | 153.77 | 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 | 15 | 223.77 | 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 | 41235 | A | C | 10 | 132.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3800 | 15806 | A | C | 250 | 611.77 | noncoding | Transversion | 0/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) |
| Scaffold_3800 | 15807 | A | T | 250 | 786.77 | noncoding | Transversion | 0/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) |
| Scaffold_3803 | 20618 | G | T | 43 | 119.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3803 | 20645 | G | C | 42 | 389.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3803 | 20686 | T | A | 23 | 129.77 | noncoding | Transversion | 0/1 | Unannotated |