| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_335 | 52703 | G | C | 23 | 221.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_335 | 52814 | T | A | 12 | 95.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_337 | 30871 | C | G | 31 | 977.77 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_337 | 32872 | A | T | 15 | 42.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_338 | 51799 | C | A | 13 | 467.77 | exon | Transversion | 1/1 | Probable zinc metalloprotease EGY2, chloroplastic (EC 3.4.24.-) (Protein ETHYLENE-DEPENDENT GRAVITROPISM-DEFICIENT AND YELLOW-GREEN 2) |
| Scaffold_341 | 30426 | A | T | 17 | 156.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_343 | 65268 | T | G | 34 | 1183.77 | CDS | Transversion | 1/1 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_343 | 79717 | A | T | 48 | 947.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_343 | 79740 | G | T | 44 | 202.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_343 | 79756 | A | T | 47 | 240.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_347 | 69274 | A | C | 15 | 49.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_349 | 36658 | G | C | 19 | 308.77 | exon | Transversion | 0/1 | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorganic pyrophosphatase) (H(+)-PPase) (Vacuolar H(+)-pyrophosphatase) |
| Scaffold_349 | 36673 | C | A | 11 | 51.77 | exon | Transversion | 0/1 | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorganic pyrophosphatase) (H(+)-PPase) (Vacuolar H(+)-pyrophosphatase) |
| Scaffold_350 | 68645 | T | G | 27 | 59.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_350 | 68646 | A | T | 31 | 115.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_359 | 5158 | C | A | 48 | 1294.77 | CDS | Transversion | 1/1 | Polyadenylate-binding protein RBP47B' (Poly(A)-binding protein RBP47B') (RNA-binding protein 47B') (AtRBP47B prime) (AtRBP47B') |
| Scaffold_367 | 15663 | C | A | 135 | 3575.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_376 | 63370 | C | G | 20 | 40.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_378 | 15743 | G | T | 14 | 259.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_378 | 15833 | C | G | 23 | 299.77 | noncoding | Transversion | 0/1 | Unannotated |