| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1302 | 2749 | A | T | 45 | 179.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1306 | 48546 | A | C | 13 | 42.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1308 | 44077 | T | A | 250 | 2382.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1314 | 35187 | G | C | 32 | 806.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1314 | 35189 | T | G | 20 | 389.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1315 | 20847 | C | G | 22 | 124.77 | 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_1318 | 37629 | A | C | 19 | 291.77 | noncoding | Transversion | 0/1 | Isoflavone 3'-hydroxylase (EC 1.14.13.52) (Cytochrome P450 81E9) (Fragment) |
| Scaffold_1318 | 37631 | A | T | 26 | 452.77 | noncoding | Transversion | 0/1 | Isoflavone 3'-hydroxylase (EC 1.14.13.52) (Cytochrome P450 81E9) (Fragment) |
| Scaffold_1328 | 28663 | A | C | 23 | 406.79 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1353 | 19477 | T | G | 13 | 103.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1353 | 19478 | C | A | 15 | 128.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1354 | 33487 | T | G | 133 | 44.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1360 | 34773 | T | A | 88 | 260.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1371 | 50595 | A | C | 67 | 84.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1388 | 45913 | A | T | 27 | 485.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1392 | 158 | G | C | 121 | 2498.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1392 | 313 | C | G | 90 | 114.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1392 | 318 | T | A | 78 | 92.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_1396 | 28797 | T | A | 49 | 146.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_1397 | 6282 | T | A | 14 | 70.77 | intron | Transversion | 0/1 | Unannotated |