| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2938 | 47267 | G | A | 175 | 626.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2938 | 48191 | G | A | 27 | 178.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2938 | 48314 | G | A | 12 | 152.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2942 | 25425 | C | T | 11 | 143.77 | exon | Transition | 0/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_2942 | 33420 | C | T | 250 | 3263.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_2943 | 13250 | G | A | 198 | 7404.77 | CDS | Transition | 1/1 | Unannotated |
| Scaffold_2947 | 4920 | C | T | 19 | 209.77 | noncoding | Transition | 0/1 | 30S ribosomal protein S2, chloroplastic |
| Scaffold_2962 | 9399 | T | C | 249 | 9046.77 | noncoding | Transition | 1/1 | Unannotated |
| Scaffold_2963 | 17595 | G | A | 250 | 3975.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2963 | 17757 | T | C | 12 | 120.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2964 | 16100 | C | T | 246 | 489.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_2964 | 16163 | C | T | 64 | 1572.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16166 | C | T | 62 | 1130.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16196 | C | T | 186 | 6663.77 | noncoding | Transition | 1/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16225 | C | T | 250 | 8893.77 | noncoding | Transition | 1/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16251 | C | T | 250 | 363.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16322 | C | T | 173 | 4539.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16334 | C | T | 136 | 2768.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16355 | C | T | 84 | 1094.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |
| Scaffold_2964 | 16358 | C | T | 106 | 1952.77 | noncoding | Transition | 0/1 | ATP synthase protein MI25 (ORF 25) |