| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2416 | 66195 | C | A | 11 | 309.56 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2417 | 135666 | T | A | 31 | 204.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2417 | 135811 | A | C | 17 | 437.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2417 | 135822 | T | G | 12 | 208.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2417 | 139193 | T | A | 23 | 341.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2419 | 144144 | A | C | 12 | 61.77 | exon | Transversion | 0/1 | Protein FAR-RED ELONGATED HYPOCOTYL 3 |
| Scaffold_2419 | 144428 | G | C | 11 | 61.77 | CDS | Transversion | 0/1 | Protein FAR-RED ELONGATED HYPOCOTYL 3 |
| Scaffold_2422 | 105791 | G | T | 248 | 575.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2422 | 126565 | T | A | 17 | 61.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2422 | 126566 | T | G | 17 | 61.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2422 | 134336 | A | T | 20 | 40.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2423 | 110746 | C | G | 21 | 34.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2425 | 33738 | T | G | 250 | 8714.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2426 | 23107 | G | C | 23 | 57.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2426 | 105982 | G | C | 28 | 56.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2426 | 126051 | T | G | 21 | 48.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2426 | 126123 | T | G | 18 | 30.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2426 | 139236 | G | C | 10 | 67.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2428 | 43725 | A | T | 22 | 86.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2430 | 44308 | T | A | 29 | 31.77 | noncoding | Transversion | 0/1 | Unannotated |