| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2934 | 39078 | C | A | 43 | 470.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2938 | 41707 | G | C | 28 | 74.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2942 | 25492 | C | G | 12 | 224.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_2943 | 12978 | T | A | 250 | 8964.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_2945 | 6264 | G | C | 94 | 186.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2953 | 5701 | C | A | 91 | 3302.77 | noncoding | Transversion | 1/1 | NAD(P)H-quinone oxidoreductase chain 4, chloroplastic (EC 7.1.1.-) (NAD(P)H dehydrogenase, chain 4) (NADH-plastoquinone oxidoreductase chain 4) |
| Scaffold_2953 | 22199 | A | C | 11 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2962 | 9401 | T | A | 250 | 8602.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_2962 | 9408 | A | T | 250 | 54.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2963 | 2192 | T | G | 38 | 1186.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_2963 | 17596 | G | T | 247 | 295.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2971 | 8042 | T | G | 151 | 52.74 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_2971 | 36778 | G | C | 35 | 433.77 | intron | Transversion | 0/1 | ATP-dependent zinc metalloprotease FTSH 2, chloroplastic (OsFTSH2) (EC 3.4.24.-) |
| Scaffold_2976 | 49730 | C | A | 24 | 176.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2993 | 24174 | A | T | 250 | 372.77 | noncoding | Transversion | 0/1 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) |
| Scaffold_2993 | 24175 | T | A | 250 | 705.77 | noncoding | Transversion | 0/1 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) |
| Scaffold_3008 | 33842 | T | A | 10 | 212.8 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3008 | 33843 | A | C | 24 | 519.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3010 | 49640 | A | C | 250 | 73.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3010 | 49643 | G | T | 250 | 32.77 | noncoding | Transversion | 0/1 | Unannotated |