| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_105 | 286654 | T | C | 250 | 284.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_105 | 286793 | T | C | 213 | 618.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_105 | 287747 | T | C | 250 | 194.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_106 | 34513 | A | G | 20 | 128.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_106 | 128823 | C | T | 17 | 63.77 | CDS | Transition | 0/1 | DNA-directed RNA polymerase 3B, chloroplastic (EC 2.7.7.6) (NictaRpoT3-tom) (T7 bacteriophage-type single subunit RNA polymerase 3B) |
| Scaffold_106 | 128851 | C | T | 44 | 151.77 | CDS | Transition | 0/1 | DNA-directed RNA polymerase 3B, chloroplastic (EC 2.7.7.6) (NictaRpoT3-tom) (T7 bacteriophage-type single subunit RNA polymerase 3B) |
| Scaffold_106 | 156488 | G | A | 21 | 274.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_106 | 175380 | T | C | 24 | 33.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_106 | 176185 | T | C | 38 | 30.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_106 | 318816 | G | A | 22 | 52.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_106 | 319482 | A | G | 78 | 1113.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_106 | 319504 | A | G | 49 | 806.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_106 | 319613 | T | C | 104 | 1397.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_106 | 319751 | C | T | 66 | 454.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_107 | 133086 | G | A | 17 | 77.77 | intron | Transition | 0/1 | Protein SPIRRIG (BEACH domain-containing protein A1) (BEACH-domain homolog A1) |
| Scaffold_107 | 163887 | C | T | 250 | 624.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_107 | 182255 | A | G | 10 | 85.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_107 | 182261 | G | A | 46 | 185.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_107 | 253942 | T | C | 12 | 68.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_107 | 269932 | G | A | 29 | 434.77 | intron | Transition | 0/1 | Unannotated |