| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2549 | 73600 | T | A | 11 | 36.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2553 | 41609 | C | A | 69 | 154.77 | CDS | Transversion | 0/1 | UPF0603 protein OsI_019212, chloroplastic |
| Scaffold_2556 | 16944 | A | C | 78 | 2622.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2558 | 46720 | C | A | 14 | 58.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2558 | 49107 | A | T | 20 | 46.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2559 | 96466 | T | A | 17 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2560 | 92900 | G | C | 16 | 490.96 | CDS | Transversion | 1/1 | 12-oxophytodienoate reductase 2 (EC 1.3.1.42) (12-oxophytodienoate-10,11-reductase 2) (AtOPR2) (OPDA-reductase 2) (4,5-didehydrojasmonate reductase) (EC 1.3.1.-) |
| Scaffold_2561 | 20329 | T | G | 20 | 40.77 | exon | Transversion | 0/1 | Trans-cinnamate 4-monooxygenase (EC 1.14.14.91) (Cinnamic acid 4-hydroxylase) (C4H) (CA4H) (Cytochrome P450 73) (Cytochrome P450C4H) |
| Scaffold_2561 | 20330 | G | C | 20 | 40.77 | exon | Transversion | 0/1 | Trans-cinnamate 4-monooxygenase (EC 1.14.14.91) (Cinnamic acid 4-hydroxylase) (C4H) (CA4H) (Cytochrome P450 73) (Cytochrome P450C4H) |
| Scaffold_2562 | 20213 | T | G | 21 | 600.28 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2566 | 90412 | G | T | 70 | 2206.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2568 | 74789 | A | C | 29 | 53.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2570 | 61324 | C | G | 14 | 245.77 | CDS | Transversion | 0/1 | Cell division cycle 20.1, cofactor of APC complex (AtCDC20.1) |
| Scaffold_2570 | 61360 | G | T | 50 | 54.77 | CDS | Transversion | 0/1 | Cell division cycle 20.1, cofactor of APC complex (AtCDC20.1) |
| Scaffold_2570 | 61372 | T | A | 56 | 89.77 | CDS | Transversion | 0/1 | Cell division cycle 20.1, cofactor of APC complex (AtCDC20.1) |
| Scaffold_2571 | 20289 | T | G | 13 | 73.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2573 | 7245 | A | T | 19 | 49.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2573 | 7343 | C | A | 10 | 61.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2573 | 7345 | T | A | 10 | 61.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2577 | 102649 | C | A | 10 | 67.77 | CDS | Transversion | 0/1 | Unannotated |