| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_146 | 377266 | A | T | 44 | 91.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_146 | 391464 | A | T | 12 | 302.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_147 | 181964 | G | C | 11 | 81.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_147 | 227474 | A | C | 17 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_147 | 228301 | T | A | 18 | 37.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_147 | 580013 | A | T | 38 | 44.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_147 | 580112 | T | G | 15 | 123.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_148 | 450416 | C | A | 157 | 4645.77 | exon | Transversion | 1/1 | Protein PLASTID TRANSCRIPTIONALLY ACTIVE 10 (pTAC10) (Plastid-encoded RNA polymerase-associated protein 3) (PEP-associated protein 3) (Protein PIGMENT DEFECTIVE 312) |
| Scaffold_149 | 52706 | G | T | 17 | 522.1 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_149 | 128071 | C | G | 10 | 103.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_149 | 267378 | C | A | 19 | 89.77 | exon | Transversion | 0/1 | Protein EXECUTER 2, chloroplastic (OsEX2) |
| Scaffold_149 | 288665 | T | G | 10 | 70.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_149 | 288666 | C | A | 10 | 67.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_149 | 454069 | C | G | 17 | 37.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 31017 | T | G | 17 | 43.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 163994 | G | C | 14 | 126.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 254301 | T | A | 22 | 40.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 262104 | T | G | 10 | 92.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 262233 | C | G | 82 | 173.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_150 | 279048 | T | G | 23 | 37.77 | CDS | Transversion | 0/1 | Unannotated |