| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3172 | 18319 | G | T | 12 | 123.77 | noncoding | Transversion | 0/1 | Adenylate kinase 2, chloroplastic (AK 2) (EC 2.7.4.3) (ATP-AMP transphosphorylase 2) (ATP:AMP phosphotransferase) (Adenylate monophosphate kinase 2) (AMK2) |
| Scaffold_3173 | 37155 | C | G | 96 | 3466.77 | noncoding | Transversion | 1/1 | 30S ribosomal protein S2, chloroplastic |
| Scaffold_3173 | 37156 | T | G | 94 | 3333.77 | noncoding | Transversion | 1/1 | 30S ribosomal protein S2, chloroplastic |
| Scaffold_3176 | 66833 | C | A | 12 | 312.78 | exon | Transversion | 1/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3176 | 66926 | C | G | 12 | 309.78 | exon | Transversion | 1/1 | Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Reverse transcriptase (EC 2.7.7.49); Endonuclease] |
| Scaffold_3177 | 25794 | A | T | 48 | 88.77 | CDS | Transversion | 0/1 | Puromycin-sensitive aminopeptidase (PSA) (EC 3.4.11.14) (Cytosol alanyl aminopeptidase) (AAP-S) (Meiotic prophase aminopeptidase 1) |
| Scaffold_3179 | 5904 | G | T | 15 | 544.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3180 | 7428 | T | G | 113 | 1849.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 7429 | G | T | 101 | 1055.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 32903 | A | C | 250 | 50.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 32904 | A | T | 250 | 32.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 33481 | A | T | 27 | 862.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3180 | 33561 | A | T | 249 | 200.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 33872 | T | G | 102 | 129.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3181 | 40072 | T | A | 22 | 615.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3181 | 40077 | A | T | 22 | 645.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3184 | 42312 | C | G | 23 | 621.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3185 | 241 | T | G | 10 | 177.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3185 | 455 | G | T | 14 | 223.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |
| Scaffold_3185 | 577 | T | G | 13 | 149.77 | exon | Transversion | 0/1 | Retrovirus-related Pol polyprotein from transposon RE2 (Retro element 2) (AtRE2) [Includes: Protease RE2 (EC 3.4.23.-); Reverse transcriptase RE2 (EC 2.7.7.49); Endonuclease RE2] |