| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3640 | 12478 | T | C | 39 | 31.77 | CDS | Transition | 0/1 | Cell division protein FtsZ homolog 1, chloroplastic (AtFtsZ1) (AtFtsZ1-1) (Chloroplast FtsZ) (CpFtsZ) (Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 10) (Protein PLASTID MOVEMENT IMPAIRED4) |
| Scaffold_3641 | 1877 | A | G | 15 | 246.77 | noncoding | Transition | 0/1 | Putative methylesterase 14, chloroplastic (AtMES14) (EC 3.1.1.-) |
| Scaffold_3641 | 1915 | T | C | 36 | 794.77 | noncoding | Transition | 0/1 | Putative methylesterase 14, chloroplastic (AtMES14) (EC 3.1.1.-) |
| Scaffold_3641 | 2530 | C | T | 12 | 276.22 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3641 | 2539 | T | C | 14 | 36.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3641 | 2576 | C | T | 51 | 822.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3651 | 3008 | G | A | 35 | 591.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3651 | 3086 | T | C | 39 | 372.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3651 | 3486 | C | T | 82 | 126.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3651 | 3581 | A | G | 59 | 544.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3663 | 4598 | A | G | 24 | 40.77 | noncoding | Transition | 0/1 | Unannotated |
| Scaffold_3663 | 21829 | A | G | 250 | 3050.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21891 | T | C | 81 | 1137.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 22800 | A | G | 50 | 178.77 | CDS | Transition | 0/1 | Novel plant SNARE 12 (AtNPSN12) |
| Scaffold_3663 | 22802 | A | G | 48 | 178.77 | CDS | Transition | 0/1 | Novel plant SNARE 12 (AtNPSN12) |
| Scaffold_3664 | 13777 | G | A | 15 | 181.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6553 | C | T | 97 | 1387.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6567 | T | C | 86 | 893.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6665 | G | A | 142 | 899.77 | CDS | Transition | 0/1 | Unannotated |
| Scaffold_3673 | 6765 | T | C | 13 | 108.77 | intron | Transition | 0/1 | Unannotated |