| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1271 | 44090 | A | G | 72 | 288.77 | CDS | Transition | 0/1 | Probable fructokinase-7 (EC 2.7.1.4) |
| Scaffold_1271 | 44746 | G | A | 24 | 478.77 | CDS | Transition | 0/1 | Probable fructokinase-7 (EC 2.7.1.4) |
| Scaffold_1273 | 6803 | A | G | 31 | 509.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1274 | 8363 | C | T | 110 | 2667.77 | exon | Transition | 0/1 | Protein phosphatase 1 regulatory subunit INH3 (Protein INHIBITOR-3) (AtINH3) |
| Scaffold_1276 | 34985 | T | C | 18 | 31.77 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon RE1 (Retro element 1) (AtRE1) [Includes: Protease RE1 (EC 3.4.23.-); Reverse transcriptase RE1 (EC 2.7.7.49); Endonuclease RE1] |
| Scaffold_1278 | 2820 | C | T | 73 | 993.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1285 | 8104 | A | G | 128 | 42.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1296 | 29914 | C | T | 15 | 230.96 | intron | Transition | 0/1 | Unannotated |
| Scaffold_1296 | 29915 | A | C,T | 28 | 855.77 | intron | Transition | 1/2 | Unannotated |
| Scaffold_1297 | 23739 | A | G | 22 | 337.77 | CDS | Transition | 0/1 | Probable aquaporin PIP2-2 (OsPIP2;2) (Plasma membrane intrinsic protein 2-2) |
| Scaffold_1299 | 35312 | G | A | 90 | 66.77 | noncoding | Transition | 0/1 | Phosphoglucan phosphatase DSP4, chloroplastic (EC 3.1.3.-) (AtPTPKIS1) (Dual specificity protein phosphatase 4) (Protein STARCH-EXCESS 4) (AtSEX4) |
| Scaffold_1302 | 3771 | C | T | 52 | 245.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_1303 | 35543 | G | A | 15 | 189.77 | exon | Transition | 0/1 | Chromoplast-specific carotenoid-associated protein, chromoplastic |
| Scaffold_1306 | 48547 | C | T | 14 | 131.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 43546 | A | G | 250 | 293.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 43967 | A | G | 250 | 152.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44089 | C | T | 250 | 526.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44197 | T | C | 250 | 646.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44205 | T | C | 244 | 5262.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_1308 | 44221 | A | G | 241 | 4099.77 | CDS | Transition | 0/1 | Unannotated |