| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_55 | 31028 | T | C | 14 | 148.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 218132 | T | C | 12 | 234.98 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_55 | 283787 | T | C | 13 | 225.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 286873 | A | G | 38 | 60.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_55 | 333507 | G | A | 20 | 168.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_55 | 334038 | A | G | 15 | 191.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 334060 | G | A | 19 | 220.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 662481 | G | A | 41 | 105.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_55 | 671307 | C | T | 99 | 213.77 | CDS | Transition | 0/1 | Pentatricopeptide repeat-containing protein At4g18520, chloroplastic (Protein PIGMENT-DEFICIENT MUTANT 1) (Protein SEEDLING LETHAL 1) |
| Scaffold_55 | 671619 | G | A | 96 | 751.77 | CDS | Transition | 0/1 | Pentatricopeptide repeat-containing protein At4g18520, chloroplastic (Protein PIGMENT-DEFICIENT MUTANT 1) (Protein SEEDLING LETHAL 1) |
| Scaffold_55 | 1030003 | C | T | 74 | 316.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 1030006 | T | C | 50 | 209.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_55 | 1365168 | C | T | 59 | 75.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_56 | 170427 | G | A | 72 | 212.77 | CDS | Transition | 0/1 | ATP-dependent zinc metalloprotease FTSH 7, chloroplastic (OsFTSH7) (EC 3.4.24.-) |
| Scaffold_56 | 173210 | T | C | 132 | 155.77 | CDS | Transition | 0/1 | ATP-dependent zinc metalloprotease FTSH 7, chloroplastic (OsFTSH7) (EC 3.4.24.-) |
| Scaffold_56 | 678911 | A | G | 49 | 69.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_56 | 728946 | C | T | 10 | 44.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_56 | 728951 | A | G | 21 | 58.77 | intron | Transition | 0/1 | Unannotated |
| Scaffold_56 | 746160 | A | G | 82 | 438.77 | exon | Transition | 0/1 | Unannotated |
| Scaffold_56 | 885223 | A | G | 250 | 2008.77 | exon | Transition | 0/1 | Unannotated |