| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3805 | 5117 | G | T | 250 | 9818.77 | intron | Transversion | 1/1 | NAD(P)H-quinone oxidoreductase subunit I, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) (NDH subunit I) (NADH-plastoquinone oxidoreductase subunit I) |
| Scaffold_3805 | 5245 | C | A | 92 | 3552.77 | intron | Transversion | 1/1 | NAD(P)H-quinone oxidoreductase subunit I, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) (NDH subunit I) (NADH-plastoquinone oxidoreductase subunit I) |
| Scaffold_3805 | 5248 | G | C | 80 | 3130.77 | intron | Transversion | 1/1 | NAD(P)H-quinone oxidoreductase subunit I, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) (NDH subunit I) (NADH-plastoquinone oxidoreductase subunit I) |
| Scaffold_3806 | 44115 | T | G | 108 | 3227.04 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3808 | 40830 | A | C | 24 | 763.78 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3809 | 7614 | T | G | 17 | 347.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3810 | 783 | G | C | 57 | 367.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3810 | 847 | A | T | 21 | 304.77 | CDS | Transversion | 0/1 | Unannotated |
| Scaffold_3811 | 56925 | T | G | 13 | 67.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3813 | 54226 | C | G | 85 | 3013.77 | noncoding | Transversion | 1/1 | Protein TIC 214 (Translocon at the inner envelope membrane of chloroplasts 214) (AtTIC214) |
| Scaffold_3814 | 73622 | G | T | 14 | 417.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3816 | 7058 | G | T | 10 | 304.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3821 | 45637 | T | A | 11 | 173.9 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3822 | 1370 | C | G | 51 | 42.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3822 | 3081 | T | G | 33 | 41.77 | noncoding | Transversion | 0/1 | NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit 5) (NADH-plastoquinone oxidoreductase subunit 5) |
| Scaffold_3823 | 21968 | C | G | 15 | 556.77 | noncoding | Transversion | 1/1 | Unannotated |
| Scaffold_3824 | 10579 | A | C | 250 | 285.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3824 | 10766 | A | C | 249 | 468.77 | noncoding | Transversion | 0/1 | Unannotated |
| Scaffold_3824 | 10789 | A | C | 250 | 1225.77 | exon | Transversion | 0/1 | Unannotated |
| Scaffold_3824 | 10843 | T | G | 249 | 43.77 | exon | Transversion | 0/1 | Unannotated |