| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_264 | 1599 | T | G | 27 | 935.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_264 | 1604 | A | C | 46 | 39.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_264 | 79488 | T | A | 44 | 48.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_266 | 44972 | G | T | 13 | 33.77 | exon | Transversion | 0/1 | Putative alpha-L-fucosidase 1 (EC 3.2.1.51) (Alpha-L-fucoside fucohydrolase) |
| Scaffold_269 | 15417 | A | T | 10 | 30.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_269 | 15418 | G | C | 10 | 30.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_285 | 7930 | A | T | 10 | 52.77 | CDS | Transversion | 0/1 | Subtilisin-like protease Glyma18g48580 (EC 3.4.21.-) [Cleaved into: Subtilase peptide GmSubPep (Glycine max subtilase peptide) (GmSubPep)] |
| Scaffold_289 | 48697 | G | T | 10 | 98.77 | exon | Transversion | 0/1 | Scarecrow-like protein 3 (AtSCL3) (GRAS family protein 5) (AtGRAS-5) |
| Scaffold_289 | 48798 | T | G | 26 | 71.77 | exon | Transversion | 0/1 | Scarecrow-like protein 3 (AtSCL3) (GRAS family protein 5) (AtGRAS-5) |
| Scaffold_289 | 48799 | T | A | 26 | 74.77 | exon | Transversion | 0/1 | Scarecrow-like protein 3 (AtSCL3) (GRAS family protein 5) (AtGRAS-5) |
| Scaffold_290 | 82538 | C | G | 11 | 30.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_290 | 82539 | T | A | 11 | 30.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_291 | 53849 | T | G | 15 | 80.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_292 | 10612 | C | A | 10 | 30.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_292 | 15045 | G | C | 15 | 36.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_294 | 15303 | C | G | 23 | 232.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_294 | 27563 | T | A | 13 | 49.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_296 | 22192 | T | G | 37 | 163.77 | noncoding | Transversion | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 22259 | C | G | 41 | 1074.77 | noncoding | Transversion | 0/1 | BTB/POZ domain-containing protein At2g30600 |
| Scaffold_296 | 22346 | T | A | 33 | 90.77 | noncoding | Transversion | 0/1 | BTB/POZ domain-containing protein At2g30600 |