| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_242 | 73740 | A | C | 250 | 265.77 | exon | Transversion | 0/1 | 28 kDa ribonucleoprotein, chloroplastic (28RNP) |
| Scaffold_243 | 71111 | G | C | 14 | 312.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_244 | 11819 | A | C | 26 | 176.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_244 | 56443 | A | C | 12 | 51.77 | CDS | Transversion | 0/1 | Zinc finger CCCH domain-containing protein 40 (OsC3H40) |
| Scaffold_244 | 56458 | C | A | 21 | 146.77 | CDS | Transversion | 0/1 | Zinc finger CCCH domain-containing protein 40 (OsC3H40) |
| Scaffold_248 | 2994 | T | G | 25 | 480.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_249 | 12158 | T | G | 12 | 40.77 | noncoding | Transversion | 0/1 | Holliday junction resolvase MOC1, chloroplastic (EC 3.1.22.4) (Protein MONOKARYOTIC CHLOROPLAST 1) (AtMOC1) |
| Scaffold_251 | 54956 | A | T | 20 | 41.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_251 | 54959 | A | C | 23 | 55.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_251 | 84350 | A | C | 31 | 150.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_251 | 85015 | C | G | 18 | 224.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_264 | 1599 | T | G | 77 | 365.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_270 | 55631 | T | A | 250 | 135.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_273 | 51621 | T | G | 20 | 176.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_273 | 55272 | A | C | 18 | 68.77 | intron | Transversion | 0/1 | WPP domain-interacting protein 3 |
| Scaffold_285 | 25356 | T | A | 11 | 90.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_286 | 24686 | C | A | 81 | 183.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_287 | 846 | C | A | 25 | 57.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_288 | 53589 | T | G | 35 | 100.77 | exon | Transversion | 0/1 | Putative bark agglutinin LECRPA3 (Fragment) |
| Scaffold_289 | 27177 | A | T | 38 | 346.77 | intron | Transversion | 0/1 | F-box protein SKIP23 (SKP1-interacting partner 23) |