| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3306 | 39710 | C | G | 23 | 690.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3306 | 40326 | A | T | 13 | 396.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_3307 | 60581 | G | T | 11 | 396.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3312 | 7616 | C | A | 194 | 144.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3312 | 8989 | G | T | 193 | 1643.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3315 | 35171 | T | A | 14 | 193.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3320 | 29338 | C | G | 15 | 512.77 | noncoding | Transversion | 1/1 | DNA-directed RNA polymerase subunit beta'' (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit beta'') (RNA polymerase subunit beta'') |
| Scaffold_3320 | 29340 | G | T | 18 | 611.77 | noncoding | Transversion | 1/1 | DNA-directed RNA polymerase subunit beta'' (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit beta'') (RNA polymerase subunit beta'') |
| Scaffold_3321 | 33105 | T | A | 10 | 267.8 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3321 | 33304 | G | T | 11 | 237.84 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3323 | 19174 | C | A | 16 | 575.77 | CDS | Transversion | 1/1 | Trigger factor-like protein TIG, Chloroplastic (EC 5.2.1.8) (Immunophilin TIG) (Peptidyl-prolyl cis-trans isomerase TIG) (PPIase TIG) (Rotamase) |
| Scaffold_3323 | 38797 | C | G | 15 | 203.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3325 | 28549 | A | C | 12 | 306.78 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3325 | 60541 | C | G | 10 | 254.8 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_3326 | 12682 | T | G | 33 | 123.77 | CDS | Transversion | 0/1 | COP1-interactive protein 1 |
| Scaffold_3326 | 12702 | G | T | 35 | 624.77 | CDS | Transversion | 0/1 | COP1-interactive protein 1 |
| Scaffold_3328 | 27773 | T | G | 19 | 296.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3329 | 19094 | T | G | 55 | 1898.77 | noncoding | Transversion | 1/1 | FRIGIDA-like protein 3 |
| Scaffold_3330 | 2305 | G | C | 40 | 1267.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3332 | 24016 | G | T | 18 | 411.77 | CDS | Transversion | 1/1 | Uncharacterized mitochondrial protein AtMg00860 (ORF158) |