| SNPs Id | Position | Function |
| Scaffold_327 | 49676 | Cation-chloride cotransporter 1 (AtCCC1) (Protein HAPLESS 5) |
| Scaffold_339 | 74236 | 50S ribosomal protein L35, chloroplastic |
| Scaffold_343 | 65282 | Unannotated |
| Scaffold_343 | 80158 | Unannotated |
| Scaffold_349 | 6881 | Unannotated |
| Scaffold_364 | 64522 | Unannotated |
| Scaffold_370 | 4865 | NAC domain-containing protein 22 (ONAC022) |
| Scaffold_374 | 49303 | Unannotated |
| Scaffold_378 | 52225 | Unannotated |
| Scaffold_390 | 13986 | Unannotated |
| Scaffold_392 | 34895 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_392 | 55883 | Unannotated |
| Scaffold_417 | 14408 | Protein TOC75-3, chloroplastic (75 kDa translocon at the outer-envelope-membrane of chloroplasts 3) (AtTOC75-III) |
| Scaffold_420 | 9337 | Unannotated |
| Scaffold_421 | 10214 | Zinc finger protein ZAT4 |
| Scaffold_431 | 4246 | Unannotated |
| Scaffold_447 | 13564 | Calmodulin-1 (CaM-1) |
| Scaffold_448 | 62530 | Unannotated |
| Scaffold_458 | 30182 | Pheophytinase, chloroplastic (EC 3.1.1.-) (Pheophytin pheophorbide hydrolase) (Protein CO-REGULATED WITH NYE1) |
| Scaffold_475 | 8716 | Eukaryotic peptide chain release factor subunit 1-3 (Eukaryotic release factor 1-3) (eRF1-3) (Omnipotent suppressor protein 1 homolog 3) (SUP1 homolog 3) |