| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1314 | 35187 | G | C | 12 | 138.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1315 | 20847 | C | G | 10 | 141.77 | exon | Transversion | 0/1 | Serine/threonine-protein kinase SAPK10 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein kinase 10) (stress-activated protein kinase 10) (OsSAPK10) |
| Scaffold_1315 | 28889 | G | C | 52 | 60.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1328 | 28880 | G | T | 243 | 1041.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1328 | 28881 | A | C | 243 | 979.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1351 | 34257 | T | G | 18 | 40.77 | exon | Transversion | 0/1 | Potassium channel AKT6 (Potassium channel SPIK) (Shaker pollen inward rectifier K(+) channel) |
| Scaffold_1356 | 29505 | T | G | 12 | 64.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1361 | 17569 | T | G | 23 | 46.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1385 | 17187 | A | T | 15 | 92.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1385 | 17189 | T | A | 18 | 182.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_1387 | 1379 | C | A | 15 | 286.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1387 | 7794 | C | A | 14 | 98.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1387 | 7795 | T | G | 14 | 95.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1391 | 14916 | T | G | 25 | 46.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1412 | 1141 | T | G | 14 | 33.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1413 | 45359 | A | T | 95 | 2379.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1422 | 1085 | C | A | 10 | 115.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1431 | 48845 | G | C | 31 | 47.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1461 | 33540 | T | G | 11 | 304.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1476 | 14111 | G | C | 10 | 143.77 | CDS | Transversion | 0/1 | Probable phosphoribosylformylglycinamidine synthase, chloroplastic/mitochondrial (FGAM synthase) (FGAMS) (EC 6.3.5.3) (Formylglycinamide ribonucleotide amidotransferase) (FGAR amidotransferase) (FGAR-AT) (Formylglycinamide ribotide amidotransferase) |