| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2971 | 36778 | G | C | 57 | 235.77 | intron | Transversion | 0/1 | ATP-dependent zinc metalloprotease FTSH 2, chloroplastic (OsFTSH2) (EC 3.4.24.-) |
| Scaffold_2971 | 36779 | A | C | 35 | 321.77 | intron | Transversion | 0/1 | ATP-dependent zinc metalloprotease FTSH 2, chloroplastic (OsFTSH2) (EC 3.4.24.-) |
| Scaffold_2974 | 43254 | A | C | 15 | 128.77 | exon | Transversion | 0/1 | Dihydroceramide fatty acyl 2-hydroxylase FAH1 (EC 1.14.18.7) (Fatty acid 2-hydroxylase 1) (AtFAH1) |
| Scaffold_2978 | 41668 | G | C | 250 | 581.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_2980 | 16040 | C | G | 11 | 93.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_2998 | 38241 | T | G | 16 | 373.79 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_2998 | 38327 | T | G | 27 | 172.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3001 | 43595 | A | C | 38 | 118.77 | exon | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3001 | 43748 | G | T | 22 | 59.77 | exon | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3001 | 43815 | T | G | 10 | 54.77 | exon | Transversion | 0/1 | Pentatricopeptide repeat-containing protein At1g62930, chloroplastic |
| Scaffold_3004 | 40935 | C | A | 11 | 56.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3004 | 41009 | G | C | 34 | 381.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3004 | 41065 | G | T | 36 | 343.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3010 | 49641 | G | C | 250 | 148.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3010 | 49900 | T | G | 42 | 110.22 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3021 | 10713 | G | T | 27 | 189.77 | intron | Transversion | 0/1 | Unannotated |
| Scaffold_3025 | 43857 | A | C | 92 | 1606.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3025 | 44284 | G | C | 13 | 122.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3026 | 13688 | T | A | 29 | 569.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3027 | 52345 | A | T | 159 | 2784.77 | exon | Transversion | 0/1 | Unannotated |