| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_12 | 357161 | T | A | 28 | 546.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 357207 | G | T | 37 | 235.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 358037 | T | G | 18 | 269.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 358074 | T | A | 30 | 370.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 359231 | T | G | 25 | 80.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 359248 | G | T | 26 | 82.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 576156 | A | C | 15 | 501.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_12 | 722336 | T | G | 12 | 274.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 818334 | T | G | 14 | 235.8 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 820721 | G | T | 15 | 236.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1044825 | T | A | 45 | 139.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1087050 | A | C | 36 | 55.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1115602 | A | C | 12 | 266.8 | exon | Transversion | 1/1 | LEAF RUST 10 DISEASE-RESISTANCE LOCUS RECEPTOR-LIKE PROTEIN KINASE-like 1.2 (EC 2.7.11.1) (Probable receptor-like serine/threonine-protein kinase LRK10L-1.2) |
| Scaffold_12 | 1307371 | T | G | 18 | 92.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1614017 | A | C | 21 | 573.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_12 | 1648332 | C | A | 10 | 33.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1650078 | C | G | 10 | 58.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_12 | 1687274 | G | C | 10 | 127.77 | CDS | Transversion | 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_12 | 1772147 | T | G | 156 | 5151.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_12 | 2046281 | G | C | 20 | 628.77 | noncoding | Transversion | 1/1 | Unannotated |