| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_59 | 1079347 | T | G | 250 | 7856.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_59 | 1161728 | C | G | 20 | 485.96 | intron | Transversion | 1/1 | Unannotated |
| Scaffold_59 | 1161772 | T | A | 21 | 49.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_59 | 1251547 | T | A | 40 | 60.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_59 | 1295742 | G | T | 16 | 209.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_59 | 1295900 | G | C | 18 | 631.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_59 | 1378740 | G | T | 27 | 376.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_59 | 1494228 | T | G | 12 | 315.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_60 | 370640 | A | T | 11 | 135.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_60 | 370882 | T | G | 40 | 697.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_60 | 374093 | A | T | 10 | 215.77 | intron | Transversion | 0/1 | Oxygen-evolving enhancer protein 1, chloroplastic (OEE1) (33 kDa subunit of oxygen evolving system of photosystem II) (33 kDa thylakoid membrane protein) (OEC 33 kDa subunit) |
| Scaffold_60 | 537554 | G | C | 45 | 71.77 | exon | Transversion | 0/1 | U-box domain-containing protein 25 (EC 2.3.2.27) (Plant U-box protein 25) (RING-type E3 ubiquitin transferase PUB25) |
| Scaffold_60 | 646712 | C | G | 12 | 298.77 | exon | Transversion | 0/1 | Protein indeterminate-domain 9 (ID1-like zinc finger protein 1) |
| Scaffold_60 | 647667 | T | G | 51 | 861.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_60 | 738148 | T | G | 16 | 435.77 | CDS | Transversion | 1/1 | Unannotated |
| Scaffold_60 | 793375 | A | C | 11 | 39.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_60 | 847555 | A | T | 10 | 339.78 | CDS | Transversion | 1/1 | Starch synthase 3, chloroplastic/amyloplastic (AtSS3) (EC 2.4.1.21) (Soluble starch synthase III) |
| Scaffold_60 | 1196330 | G | T | 23 | 777.77 | exon | Transversion | 1/1 | Unannotated |
| Scaffold_60 | 1302087 | T | G | 17 | 49.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_60 | 1326588 | C | A | 33 | 1115.77 | CDS | Transversion | 1/1 | Unannotated |