| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3155 | 43885 | G | T | 131 | 572.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3156 | 2043 | A | C | 116 | 1294.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3156 | 2045 | G | T | 139 | 440.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3160 | 22014 | A | T | 110 | 161.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3160 | 22431 | C | A | 123 | 2531.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3160 | 23527 | C | G | 12 | 56.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3162 | 42838 | A | T | 13 | 110.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3166 | 51209 | A | C | 18 | 300.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3166 | 51282 | T | A | 21 | 81.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3166 | 51283 | A | T | 21 | 460.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3166 | 52161 | A | T | 22 | 309.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3167 | 44681 | G | C | 18 | 309.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3167 | 44810 | T | G | 15 | 157.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3167 | 44869 | A | C | 89 | 550.77 | CDS | Transversion | 0/1 | Flavin mononucleotide hydrolase 1, chloroplatic (AtcpFHy1) (EC 3.1.3.102) (5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase) (AtcpFHy1/PyrP1) (EC 3.1.3.104) (5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate phosphatase) (ARPP phosphata |
| Scaffold_3167 | 45113 | T | A | 14 | 315.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3172 | 18319 | G | T | 17 | 108.77 | noncoding | Transversion | 0/1 | Adenylate kinase 2, chloroplastic (AK 2) (EC 2.7.4.3) (ATP-AMP transphosphorylase 2) (ATP:AMP phosphotransferase) (Adenylate monophosphate kinase 2) (AMK2) |
| Scaffold_3177 | 26700 | A | T | 97 | 944.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3177 | 26787 | G | T | 21 | 95.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3177 | 26804 | A | C | 16 | 108.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3180 | 32892 | A | T | 250 | 2448.77 | noncoding | Transversion | 0/1 | Unannotated |