| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_1943 | 6056 | G | C | 10 | 301.78 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_1943 | 6472 | G | T | 11 | 340.78 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_1945 | 16504 | C | A | 22 | 728.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1952 | 23470 | G | T | 11 | 384.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1959 | 6229 | A | T | 10 | 107.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_1959 | 6271 | T | G | 11 | 396.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1975 | 34981 | G | T | 10 | 368.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_1975 | 35082 | C | A | 47 | 1284.77 | exon | Transversion | 1/1 | Outer envelope protein 64, mitochondrial (Mitochondrial outer membrane protein 64) (mtOM64) (Translocon at the outer membrane of chloroplasts 64-V) (AtTOC64-V) |
| Scaffold_1977 | 27964 | T | A | 11 | 378.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1977 | 27965 | T | G | 11 | 346.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1996 | 13613 | A | T | 11 | 387.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_1996 | 13747 | T | A | 84 | 3011.77 | noncoding | Transversion | 1/1 | 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 | 72 | 2602.77 | noncoding | Transversion | 1/1 | 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_2397 | 181857 | T | A | 15 | 100.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 132572 | T | A | 21 | 57.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 132816 | G | C | 36 | 746.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2398 | 133960 | G | C | 17 | 432.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2399 | 112374 | A | C | 22 | 670.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_2400 | 120048 | G | T | 12 | 280.84 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_2402 | 42154 | G | T | 20 | 599.77 | exon | Transversion | 1/1 | Exocyst complex component EXO70H1 (AtExo70h1) (Exocyst subunit Exo70 family protein H1) |