| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3951 | 2280 | C | A | 18 | 259.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 35901 | G | C | 35 | 406.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 58927 | C | G | 26 | 191.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3954 | 58937 | C | G | 27 | 191.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3956 | 56150 | C | A | 12 | 64.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3956 | 56152 | T | A | 11 | 67.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3957 | 14299 | C | A | 12 | 351.56 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3957 | 17379 | A | T | 248 | 268.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3961 | 8239 | G | T | 250 | 51.77 | exon | Transversion | 0/1 | ATP synthase subunit alpha, mitochondrial |
| Scaffold_3961 | 56317 | G | T | 250 | 125.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3961 | 56332 | C | G | 250 | 127.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3962 | 28750 | A | T | 41 | 629.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 28758 | A | T | 53 | 761.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 28816 | T | A | 37 | 65.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 29254 | G | T | 45 | 679.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3962 | 29350 | C | A | 28 | 110.77 | exon | Transversion | 0/1 | Protein WHAT'S THIS FACTOR 1 homolog, chloroplastic |
| Scaffold_3969 | 44864 | T | G | 22 | 276.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3969 | 45248 | G | T | 17 | 262.77 | exon | 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_3969 | 45750 | A | C | 16 | 66.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3969 | 45965 | T | G | 33 | 120.77 | 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] |