| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3192 | 220 | C | A | 250 | 95.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3192 | 306 | C | A | 39 | 1118.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3198 | 59688 | G | T | 33 | 329.77 | noncoding | Transversion | 0/1 | DNA-directed RNA polymerase subunit beta'' (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit beta'') (RNA polymerase subunit beta'') |
| Scaffold_3199 | 58834 | T | G | 140 | 281.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3199 | 58836 | T | G | 210 | 113.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3200 | 26828 | G | T | 250 | 9495.77 | noncoding | Transversion | 1/1 | Photosystem II protein D1 (PSII D1 protein) (EC 1.10.3.9) (32 kDa thylakoid membrane protein) (Photosystem II Q(B) protein) |
| Scaffold_3200 | 26837 | A | C | 248 | 128.77 | noncoding | Transversion | 0/1 | Photosystem II protein D1 (PSII D1 protein) (EC 1.10.3.9) (32 kDa thylakoid membrane protein) (Photosystem II Q(B) protein) |
| Scaffold_3204 | 14087 | C | G | 15 | 58.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3204 | 14655 | C | G | 20 | 196.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3207 | 25381 | G | T | 247 | 7800.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3209 | 15911 | G | T | 248 | 52.74 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3209 | 26935 | T | G | 248 | 48.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20251 | G | C | 49 | 347.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20267 | A | C | 250 | 523.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20298 | A | C | 250 | 1646.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20357 | A | C | 250 | 1384.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3213 | 20371 | G | T | 250 | 646.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3215 | 5298 | T | G | 67 | 202.84 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3229 | 28554 | A | T | 10 | 129.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3230 | 5554 | G | T | 250 | 81.77 | exon | Transversion | 0/1 | Unannotated |