| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_341 | 30425 | T | C | 17 | 264.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_343 | 65144 | G | A | 18 | 42.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_343 | 65493 | T | C | 68 | 902.77 | CDS | Transition | 0/1 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_343 | 65589 | G | A | 65 | 996.77 | CDS | Transition | 0/1 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_344 | 31211 | G | A | 156 | 87.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_346 | 56483 | A | G | 16 | 36.77 | CDS | Transition | 0/1 | Probable LRR receptor-like serine/threonine-protein kinase At1g53440 (EC 2.7.11.1) |
| Scaffold_349 | 6343 | A | G | 10 | 57.77 | CDS | Transition | 0/1 | Protein TOC75-3, chloroplastic (75 kDa translocon at the outer-envelope-membrane of chloroplasts 3) (AtTOC75-III) |
| Scaffold_349 | 36672 | A | G | 67 | 234.77 | exon | Transition | 0/1 | Pyrophosphate-energized vacuolar membrane proton pump (EC 3.6.1.1) (Pyrophosphate-energized inorganic pyrophosphatase) (H(+)-PPase) (Vacuolar H(+)-pyrophosphatase) |
| Scaffold_350 | 22973 | G | A | 15 | 321.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_352 | 3281 | T | C | 10 | 52.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_355 | 15103 | C | T | 38 | 517.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_355 | 15118 | A | G | 30 | 421.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_355 | 15119 | G | A | 29 | 40.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_355 | 73872 | G | A | 62 | 1618.77 | exon | Transition | 0/1 | Polyubiquitin [Cleaved into: Ubiquitin] |
| Scaffold_362 | 28576 | T | C | 16 | 31.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_363 | 32706 | G | A | 93 | 225.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_363 | 32774 | G | A | 105 | 702.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_364 | 31287 | T | C | 21 | 436.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_366 | 30351 | A | G | 11 | 62.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_368 | 5349 | G | A | 31 | 481.77 | intron | Transition | 0/1 | Phosphoribulokinase, chloroplastic (PRK) (PRKase) (EC 2.7.1.19) (Phosphopentokinase) |