| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_8 | 2606846 | T | G | 18 | 517.77 | CDS | Transversion | 1/1 | Cytochrome P450 78A3 (EC 1.14.-.-) |
| Scaffold_8 | 2870804 | G | C | 11 | 54.77 | exon | Transversion | 0/1 | ARF guanine-nucleotide exchange factor GNOM (Pattern formation protein EMB30) (Protein EMBRYO DEFECTIVE 30) (Protein MIZU-KUSSEI2) (Protein VASCULAR NETWORK 7) |
| Scaffold_8 | 2914122 | C | G | 118 | 3590.77 | CDS | Transversion | 1/1 | Probable protein phosphatase 2C 9 (OsPP2C09) (EC 3.1.3.16) |
| Scaffold_9 | 133895 | A | C | 12 | 371.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_9 | 163949 | T | A | 22 | 83.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 167160 | A | T | 10 | 262.8 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_9 | 174754 | A | T | 10 | 362.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_9 | 175028 | T | A | 52 | 1477.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 176400 | A | T | 13 | 172.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 176401 | C | A | 14 | 209.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 511233 | C | A | 11 | 270.8 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_9 | 1019768 | G | T | 22 | 40.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1174132 | G | T | 97 | 3240.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_9 | 1261824 | T | G | 14 | 271.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1262715 | C | A | 22 | 53.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1262716 | A | T | 24 | 124.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1262717 | G | T | 30 | 571.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1388951 | T | A | 158 | 4205.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1721088 | A | T | 10 | 157.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_9 | 1875302 | A | T | 18 | 468.77 | exon | Transversion | 1/1 | Unannotated |