| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_74 | 714769 | T | C | 14 | 83.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g55890, mitochondrial |
| Scaffold_11 | 598888 | A | G | 13 | 46.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g73710 |
| Scaffold_199 | 1417 | A | G | 10 | 227.84 | exon | Transition | 1/1 | Pentatricopeptide repeat-containing protein At1g77360, mitochondrial |
| Scaffold_199 | 1690 | G | A | 11 | 32.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At1g77360, mitochondrial |
| Scaffold_1234 | 8953 | G | A | 106 | 2794.77 | exon | Transition | 1/1 | Pentatricopeptide repeat-containing protein At2g18940, chloroplastic |
| Scaffold_6 | 1729600 | A | G | 11 | 55.77 | CDS | Transition | 0/1 | Pentatricopeptide repeat-containing protein At2g27610 |
| Scaffold_168 | 551159 | T | C | 21 | 34.77 | exon | Transition | 0/1 | Pentatricopeptide repeat-containing protein At3g46790, chloroplastic (Protein CHLORORESPIRATORY REDUCTION 2) |
| Scaffold_18 | 2009053 | G | A | 37 | 943.77 | exon | Transition | 1/1 | Pentatricopeptide repeat-containing protein At3g53700, chloroplastic (Protein MATERNAL EFFECT EMBRYO ARREST 40) |
| Scaffold_18 | 2009595 | C | T | 44 | 1441.77 | exon | Transition | 1/1 | Pentatricopeptide repeat-containing protein At3g53700, chloroplastic (Protein MATERNAL EFFECT EMBRYO ARREST 40) |
| Scaffold_18 | 2009610 | G | A | 35 | 990.77 | exon | Transition | 1/1 | Pentatricopeptide repeat-containing protein At3g53700, chloroplastic (Protein MATERNAL EFFECT EMBRYO ARREST 40) |
| Scaffold_498 | 5345 | A | G | 62 | 1893.77 | CDS | Transition | 1/1 | Peroxisomal fatty acid beta-oxidation multifunctional protein MFP2 (AtMPF2) [Includes: Enoyl-CoA hydratase/3-2-trans-enoyl-CoA isomerase/3-hydroxybutyryl-CoA epimerase (EC 4.2.1.17) (EC 5.1.2.3) (EC 5.3.3.8); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)] |
| Scaffold_96 | 14494 | T | C | 13 | 349.78 | intron | Transition | 1/1 | Peroxisomal membrane protein PEX14 (Peroxin-14) (AtPEX14) (Peroxisome biogenesis protein 14) (Pex14p) (Protein PEROXISOME DEFECTIVE 2) |
| Scaffold_34 | 499184 | G | A | 20 | 600.77 | CDS | Transition | 1/1 | Phosphatidylinositol 4-kinase alpha 1 (PI4-kinase alpha 1) (PtdIns-4-kinase alpha 1) (EC 2.7.1.67) (Phosphatidylinositol 4-OH kinase alpha1) (AtPI4Kalpha1) (PI-4Kalpha1) |
| Scaffold_53 | 1353248 | G | A | 12 | 395.77 | CDS | Transition | 1/1 | Phosphatidylinositol 4-phosphate 5-kinase 9 (AtPIP5K9) (EC 2.7.1.68) (1-phosphatidylinositol 4-phosphate kinase 9) (Diphosphoinositide kinase 9) (PtdIns(4)P-5-kinase 9) |
| Scaffold_53 | 1356380 | T | C | 14 | 357.78 | CDS | Transition | 1/1 | Phosphatidylinositol 4-phosphate 5-kinase 9 (AtPIP5K9) (EC 2.7.1.68) (1-phosphatidylinositol 4-phosphate kinase 9) (Diphosphoinositide kinase 9) (PtdIns(4)P-5-kinase 9) |
| Scaffold_15 | 317184 | A | G | 17 | 589.77 | CDS | Transition | 1/1 | Phospholipase D beta 1 (AtPLDbeta1) (PLD beta 1) (PLDbeta) (EC 3.1.4.4) |
| Scaffold_15 | 317193 | T | C | 20 | 639.77 | CDS | Transition | 1/1 | Phospholipase D beta 1 (AtPLDbeta1) (PLD beta 1) (PLDbeta) (EC 3.1.4.4) |
| Scaffold_789 | 37036 | G | A | 26 | 963.77 | noncoding | Transition | 1/1 | Photosystem I assembly protein Ycf3 |
| Scaffold_789 | 37119 | A | G | 247 | 9724.77 | noncoding | Transition | 1/1 | Photosystem I assembly protein Ycf3 |
| Scaffold_3731 | 29572 | G | A | 250 | 8740.77 | noncoding | Transition | 1/1 | Photosystem I assembly protein Ycf4 |