| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3969 | 45248 | G | T | 63 | 1312.77 | 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 | 29 | 39.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3969 | 45965 | T | G | 37 | 115.77 | 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_3969 | 46167 | T | G | 79 | 1671.77 | CDS | 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_3971 | 25105 | G | C | 250 | 393.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3971 | 25397 | A | C | 250 | 2004.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3979 | 4127 | T | G | 138 | 4672.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3980 | 41371 | A | C | 36 | 700.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3980 | 41433 | C | G | 59 | 730.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3980 | 51236 | A | T | 11 | 311.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3987 | 20662 | A | C | 250 | 6371.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3987 | 20663 | G | T | 250 | 8775.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3987 | 20706 | A | C | 250 | 1182.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3991 | 21612 | A | C | 250 | 77.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3994 | 12860 | T | A | 13 | 85.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3996 | 20350 | G | C | 14 | 507.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3998 | 26458 | T | G | 143 | 4651.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3998 | 26460 | T | G | 36 | 122.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_4003 | 17061 | G | C | 29 | 791.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_4004 | 15382 | T | G | 36 | 137.77 | noncoding | Transversion | 0/1 | Unannotated |