| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2743 | 20574 | G | A | 101 | 3664.77 | intron | Transition | 1/1 | ATP synthase subunit a, chloroplastic (ATP synthase F0 sector subunit a) (F-ATPase subunit IV) |
| Scaffold_2743 | 20797 | G | A | 108 | 126.77 | noncoding | Transition | 0/1 | ATP synthase subunit a, chloroplastic (ATP synthase F0 sector subunit a) (F-ATPase subunit IV) |
| Scaffold_2765 | 26308 | G | A | 64 | 146.9 | noncoding | Transition | 1/1 | ATP synthase subunit a, chloroplastic (ATP synthase F0 sector subunit a) (F-ATPase subunit IV) |
| Scaffold_3576 | 23892 | G | A | 34 | 923.77 | noncoding | Transition | 1/1 | ATP synthase subunit a, chloroplastic (ATP synthase F0 sector subunit a) (F-ATPase subunit IV) |
| Scaffold_3611 | 1916 | T | C | 250 | 8904.77 | exon | Transition | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3611 | 2025 | C | T | 236 | 163.77 | exon | Transition | 0/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3611 | 2384 | A | G | 21 | 655.77 | CDS | Transition | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3611 | 2399 | A | G | 17 | 488.77 | CDS | Transition | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3611 | 2430 | T | C | 12 | 344.22 | CDS | Transition | 0/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3611 | 2462 | A | G | 250 | 8809.77 | CDS | Transition | 1/1 | ATP synthase subunit alpha, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit alpha) (F-ATPase subunit alpha) |
| Scaffold_3479 | 16087 | C | T | 240 | 4449.77 | noncoding | Transition | 0/1 | ATP synthase subunit alpha, mitochondrial |
| Scaffold_3934 | 42453 | C | T | 243 | 8641.77 | intron | Transition | 1/1 | ATP synthase subunit alpha, mitochondrial |
| Scaffold_185 | 15701 | T | C | 141 | 307.77 | intron | Transition | 0/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) |
| Scaffold_3800 | 15683 | G | A | 119 | 4336.77 | noncoding | Transition | 1/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) |
| Scaffold_3800 | 15684 | A | G | 250 | 9126.77 | noncoding | Transition | 1/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) |
| Scaffold_3870 | 41427 | A | G | 42 | 71.77 | noncoding | Transition | 0/1 | ATP synthase subunit beta, chloroplastic (EC 3.6.3.14) (ATP synthase F1 sector subunit beta) (F-ATPase subunit beta) (Fragment) |
| Scaffold_2993 | 23870 | C | T | 250 | 7435.77 | noncoding | Transition | 0/1 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp) |
| Scaffold_52 | 1593214 | A | G | 27 | 700.77 | CDS | Transition | 1/1 | ATP-dependent helicase BRM (EC 3.6.4.12) (Protein BRAHMA) (AtBRM) (Protein CHROMATIN REMODELING 2) (AtCHR2) |
| Scaffold_2971 | 35847 | A | G | 19 | 658.77 | noncoding | Transition | 1/1 | ATP-dependent zinc metalloprotease FTSH 12, chloroplastic (AtFTSH12) (EC 3.4.24.-) |
| Scaffold_181 | 684526 | T | C | 120 | 3526.77 | CDS | Transition | 1/1 | Auxin transport protein BIG (Protein ATTENUATED SHADE AVOIDANCE 1) (Protein CORYMBOSA1) (Protein DARK OVER-EXPRESSION OF CAB 1) (Protein LOW PHOSPHATE-RESISTANT ROOT 1) (Protein TRANSPORT INHIBITOR RESPONSE 3) (Protein UMBRELLA 1) |