| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3944 | 3526 | G | A | 170 | 5465.77 | intron | Transition | 1/1 | Unannotated |
| Scaffold_3948 | 6456 | G | A | 76 | 109.77 | exon | Transition | 0/1 | Protein transport protein SEC16A homolog (Protein MAIGO 5) |
| Scaffold_3948 | 6517 | A | G | 16 | 191.77 | exon | Transition | 0/1 | Protein transport protein SEC16A homolog (Protein MAIGO 5) |
| Scaffold_3954 | 35575 | C | T | 37 | 454.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3954 | 35642 | G | A | 11 | 32.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3954 | 43471 | T | C | 49 | 1761.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_3957 | 12921 | C | T | 20 | 378.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3957 | 12971 | A | G | 21 | 128.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3957 | 14309 | T | C | 11 | 103.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3957 | 17311 | T | C | 250 | 56.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_3961 | 8354 | C | T | 148 | 76.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3961 | 8712 | C | T | 149 | 1715.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_3961 | 9008 | C | T | 39 | 893.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3961 | 9201 | C | T | 250 | 7781.77 | noncoding | Transition | 1/1 | Ribosomal protein S1, mitochondrial |
| Scaffold_3961 | 9252 | C | T | 240 | 6220.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3961 | 56541 | T | C | 250 | 7239.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3962 | 28279 | G | A | 13 | 181.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 28354 | G | A | 24 | 338.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 28432 | T | C | 31 | 147.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 28433 | G | A | 31 | 107.77 | exon | Transition | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |