| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3469 | 46161 | A | C | 46 | 1622.77 | noncoding | Transversion | 1/1 | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit beta') (RNA polymerase subunit beta') |
| Scaffold_3470 | 18548 | C | A | 10 | 160.77 | noncoding | Transversion | 0/1 | Uncharacterized protein ycf68 (ORF133) |
| Scaffold_3470 | 18549 | G | T | 40 | 61.77 | noncoding | Transversion | 0/1 | Uncharacterized protein ycf68 (ORF133) |
| Scaffold_3471 | 23437 | T | G | 106 | 3062.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3472 | 36718 | T | A | 23 | 59.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3475 | 42727 | C | G | 26 | 758.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3475 | 42728 | T | G | 14 | 450.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3477 | 59202 | C | G | 62 | 989.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3477 | 59203 | T | G | 111 | 1992.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3477 | 62673 | T | A | 22 | 102.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3477 | 62674 | C | A | 11 | 169.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3479 | 26114 | C | A | 83 | 2163.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_3480 | 40538 | T | G | 250 | 87.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40646 | T | G | 250 | 3856.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40716 | G | C | 216 | 2792.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3480 | 40770 | T | A | 39 | 354.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3481 | 23812 | G | C | 14 | 485.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_3481 | 23813 | T | G | 12 | 372.31 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3481 | 28781 | G | C | 65 | 182.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3482 | 15166 | T | A | 32 | 31.77 | CDS | Transversion | 0/1 | Unannotated |