| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_460 | 8148 | A | C | 30 | 625.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_461 | 54393 | T | A | 60 | 1492.78 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_463 | 20850 | A | T | 126 | 1209.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_463 | 22599 | C | A | 22 | 461.74 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_463 | 22846 | A | T | 24 | 307.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_481 | 42565 | C | A | 67 | 1005.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_481 | 42567 | G | T | 31 | 237.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_484 | 30123 | C | A | 53 | 659.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_484 | 30133 | C | A | 108 | 236.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_484 | 30134 | A | T | 115 | 2722.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_484 | 30244 | A | C | 26 | 158.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_486 | 44675 | C | A | 24 | 78.77 | noncoding | Transversion | 0/1 | GDSL esterase/lipase At5g18430 (EC 3.1.1.-) (Extracellular lipase At5g18430) |
| Scaffold_486 | 44676 | A | C | 43 | 431.77 | noncoding | Transversion | 0/1 | GDSL esterase/lipase At5g18430 (EC 3.1.1.-) (Extracellular lipase At5g18430) |
| Scaffold_487 | 31865 | A | C | 10 | 48.77 | exon | Transversion | 0/1 | Protein argonaute 4A (OsAGO4a) |
| Scaffold_487 | 52012 | A | C | 11 | 163.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_487 | 66194 | C | A | 121 | 135.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_487 | 66533 | C | G | 11 | 250.31 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_494 | 50399 | T | G | 11 | 45.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_495 | 65871 | T | G | 10 | 102.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_496 | 26340 | A | T | 28 | 668.03 | exon | Transversion | 0/1 | Unannotated |