| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3010 | 49703 | T | G | 248 | 679.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3010 | 49765 | A | C | 249 | 404.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3017 | 9085 | T | A | 20 | 46.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3017 | 9086 | G | T | 20 | 37.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3017 | 45894 | G | T | 250 | 596.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3017 | 45895 | A | T | 250 | 989.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3018 | 62254 | T | G | 19 | 348.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3025 | 43826 | G | C | 11 | 127.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3025 | 43857 | A | C | 11 | 129.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3025 | 45032 | T | G | 21 | 63.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3027 | 3929 | C | G | 116 | 3891.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3027 | 4006 | C | A | 250 | 160.77 | noncoding | Transversion | 0/1 | Protein TIC 214 (Translocon at the inner envelope membrane of chloroplasts 214) (AtTIC214) |
| Scaffold_3027 | 4007 | T | A | 250 | 581.77 | noncoding | Transversion | 0/1 | Protein TIC 214 (Translocon at the inner envelope membrane of chloroplasts 214) (AtTIC214) |
| Scaffold_3027 | 52345 | A | T | 12 | 70.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3027 | 52376 | C | A | 25 | 159.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3027 | 52422 | A | T | 39 | 370.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3029 | 8316 | C | G | 26 | 822.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3034 | 21390 | A | C | 245 | 2175.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3034 | 21391 | G | T | 242 | 2080.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3039 | 51312 | T | G | 12 | 49.77 | CDS | Transversion | 0/1 | Heat shock 70 kDa protein 17 (Heat shock protein 70-17) (AtHsp70-17) |