| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_327 | 49676 | T | C | 10 | 61.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_335 | 43256 | T | C | 85 | 2674.77 | noncoding | Transition | 0/1 | Cellulose synthase A catalytic subunit 1 [UDP-forming] (AtCesA1) (EC 2.4.1.12) (Protein RADIALLY SWOLLEN 1) (AtRSW1) |
| Scaffold_335 | 43259 | G | A | 85 | 2649.77 | noncoding | Transition | 0/1 | Cellulose synthase A catalytic subunit 1 [UDP-forming] (AtCesA1) (EC 2.4.1.12) (Protein RADIALLY SWOLLEN 1) (AtRSW1) |
| Scaffold_339 | 74236 | T | C | 21 | 37.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_343 | 65282 | T | C | 13 | 32.77 | CDS | Transition | 0/1 | 3-dehydroquinate synthase, chloroplastic (EC 4.2.3.4) |
| Scaffold_343 | 80158 | A | G | 43 | 66.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_345 | 53717 | G | A | 21 | 424.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_349 | 6881 | G | A | 12 | 61.77 | CDS | Transition | 0/1 | Protein TOC75-3, chloroplastic (75 kDa translocon at the outer-envelope-membrane of chloroplasts 3) (AtTOC75-III) |
| Scaffold_355 | 73872 | G | A | 117 | 3132.77 | exon | Transition | 1/1 | Polyubiquitin [Cleaved into: Ubiquitin] |
| Scaffold_364 | 64522 | T | C | 11 | 58.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_370 | 4865 | A | G | 11 | 58.77 | exon | Transition | 0/1 | Zinc finger protein ZAT4 |
| Scaffold_374 | 49303 | T | C | 32 | 56.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_376 | 63315 | C | T | 116 | 1250.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_378 | 52225 | C | T | 80 | 204.77 | intron | Transition | 0/1 | Calmodulin-1 (CaM-1) |
| Scaffold_390 | 13986 | A | G | 20 | 37.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_392 | 34895 | T | C | 13 | 52.77 | exon | Transition | 0/1 | Pheophytinase, chloroplastic (EC 3.1.1.-) (Pheophytin pheophorbide hydrolase) (Protein CO-REGULATED WITH NYE1) |
| Scaffold_392 | 55883 | G | A | 23 | 31.77 | exon | Transition | 0/1 | Eukaryotic peptide chain release factor subunit 1-3 (Eukaryotic release factor 1-3) (eRF1-3) (Omnipotent suppressor protein 1 homolog 3) (SUP1 homolog 3) |
| Scaffold_414 | 35077 | T | C | 10 | 243.84 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_417 | 14408 | C | T | 12 | 36.77 | CDS | Transition | 0/1 | Benzyl alcohol O-benzoyltransferase (EC 2.3.1.196) (Benzoyl coenzyme A:benzyl alcohol benzoyl transferase) |
| Scaffold_420 | 9337 | G | A | 30 | 44.77 | exon | Transition | 0/1 | Mitogen-activated protein kinase kinase kinase ANP1 (EC 2.7.11.25) (Arabidopsis NPK1-related kinase 1) |