| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1996 | 13612 | T | A | 10 | 129.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1996 | 13613 | A | T | 13 | 170.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1996 | 13747 | T | A | 58 | 1176.77 | noncoding | Transversion | 0/1 | Phosphomethylpyrimidine synthase, chloroplastic (EC 4.1.99.17) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Protein PYRIMIDINE REQUIRING) (Thiamine biosynthesis protein ThiC) (Protein THIAMINE C) |
| Scaffold_1996 | 13748 | A | C | 54 | 805.77 | noncoding | Transversion | 0/1 | Phosphomethylpyrimidine synthase, chloroplastic (EC 4.1.99.17) (Hydroxymethylpyrimidine phosphate synthase) (HMP-P synthase) (HMP-phosphate synthase) (HMPP synthase) (Protein PYRIMIDINE REQUIRING) (Thiamine biosynthesis protein ThiC) (Protein THIAMINE C) |
| Scaffold_1997 | 25497 | T | G | 12 | 100.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2000 | 23181 | T | A | 11 | 218.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2020 | 12006 | G | T | 12 | 290.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2024 | 35292 | G | C | 110 | 761.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2397 | 78051 | T | A | 29 | 95.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2397 | 120042 | T | G | 32 | 324.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 6116 | A | C | 250 | 63.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 77524 | A | C | 21 | 239.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 77539 | T | G | 12 | 54.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 77634 | G | C | 13 | 63.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 77737 | T | A | 27 | 282.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 131691 | A | T | 23 | 94.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 132572 | T | A | 21 | 128.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 132816 | G | C | 24 | 405.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 133425 | G | T | 17 | 55.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 133626 | G | C | 18 | 136.77 | CDS | Transversion | 0/1 | Unannotated |