| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_2843 | 21250 | C | T | 20 | 604.77 | exon | Transition | 1/1 | Pre-mRNA cleavage factor Im 25 kDa subunit 2 |
| Scaffold_88 | 201414 | C | T | 26 | 76.77 | exon | Transition | 0/1 | Pre-mRNA-processing protein 40A (Mediator of RNA polymerase II transcription subunit 35a) |
| Scaffold_88 | 201426 | C | T | 35 | 91.77 | exon | Transition | 0/1 | Pre-mRNA-processing protein 40A (Mediator of RNA polymerase II transcription subunit 35a) |
| Scaffold_88 | 201441 | A | G | 52 | 1179.77 | exon | Transition | 0/1 | Pre-mRNA-processing protein 40A (Mediator of RNA polymerase II transcription subunit 35a) |
| Scaffold_88 | 201488 | A | G | 76 | 949.77 | exon | Transition | 0/1 | Pre-mRNA-processing protein 40A (Mediator of RNA polymerase II transcription subunit 35a) |
| Scaffold_88 | 201555 | T | C | 39 | 649.77 | exon | Transition | 0/1 | Pre-mRNA-processing protein 40A (Mediator of RNA polymerase II transcription subunit 35a) |
| Scaffold_2681 | 152818 | T | C | 45 | 1091.77 | CDS | Transition | 0/1 | Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (26S proteasome regulatory subunit RPN3) (Nuclear antigen 21D7) |
| Scaffold_3596 | 51633 | T | C | 13 | 431.53 | intron | Transition | 0/1 | Probable 2-oxoglutarate-dependent dioxygenase AOP1.2 (EC 1.14.11.-) |
| Scaffold_77 | 99962 | T | C | 40 | 1192.77 | CDS | Transition | 1/1 | Probable ADP-ribosylation factor GTPase-activating protein AGD14 (ARF GAP AGD14) (Protein ARF-GAP DOMAIN 14) (AtAGD14) (Protein ZIGA4) |
| Scaffold_1297 | 23739 | A | G | 20 | 521.77 | CDS | Transition | 0/1 | Probable aquaporin PIP2-2 (OsPIP2;2) (Plasma membrane intrinsic protein 2-2) |
| Scaffold_1112 | 16405 | A | G | 20 | 40.77 | intron | Transition | 0/1 | Probable boron transporter 6 |
| Scaffold_2820 | 23800 | T | C | 10 | 35.77 | CDS | Transition | 0/1 | Probable cadmium/zinc-transporting ATPase HMA1, chloroplastic (EC 3.6.3.3) (EC 3.6.3.5) (Protein HEAVY METAL ATPASE 1) |
| Scaffold_47 | 972897 | A | G | 15 | 301.77 | CDS | Transition | 0/1 | Probable carotenoid cleavage dioxygenase 4, chloroplastic (AtCCD4) (EC 1.14.99.-) (AtNCED4) |
| Scaffold_3663 | 21829 | A | G | 144 | 1532.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_3663 | 21891 | T | C | 15 | 163.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 1 [UDP-forming] (EC 2.4.1.12) (OsCesA1) |
| Scaffold_150 | 678069 | T | C | 28 | 972.77 | CDS | Transition | 1/1 | Probable cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (OsCesA8) |
| Scaffold_150 | 678126 | C | T | 39 | 1429.77 | CDS | Transition | 1/1 | Probable cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (OsCesA8) |
| Scaffold_150 | 678385 | T | C | 30 | 85.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (OsCesA8) |
| Scaffold_150 | 678388 | T | C | 29 | 46.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (OsCesA8) |
| Scaffold_150 | 679007 | A | G | 15 | 46.77 | CDS | Transition | 0/1 | Probable cellulose synthase A catalytic subunit 8 [UDP-forming] (EC 2.4.1.12) (OsCesA8) |