| SNP Id | Position | Reference Allele | Alternate Allele | DP | Quality | Located At | Type | Genotype | Function |
| Scaffold_3843 | 32755 | C | T | 250 | 9270.77 | noncoding | Transition | 1/1 | Ribosomal protein S3, mitochondrial |
| Scaffold_2697 | 103128 | T | C | 10 | 257.8 | exon | Transition | 1/1 | Ribosomal RNA small subunit methyltransferase, mitochondrial (EC 2.1.1.-) (18S mitochondrial rRNA (adenine(1914)-N(6)/adenine(1915)-N(6))-dimethyltransferase) (Adenosine dimethyl transferase 1B) (Dimethyladenosine transferase 1B) |
| Scaffold_3115 | 12879 | C | T | 45 | 47.77 | exon | Transition | 0/1 | RNA-directed DNA polymerase homolog (EC 2.7.7.48) (Reverse transcriptase homolog) |
| Scaffold_12 | 3475452 | C | T | 14 | 434.77 | exon | Transition | 1/1 | S-adenosylmethionine synthase (AdoMet synthase) (EC 2.5.1.6) (Methionine adenosyltransferase) (MAT) |
| Scaffold_2505 | 3946 | C | T | 22 | 681.77 | CDS | Transition | 1/1 | SART-1 family protein DOT2 (Protein DEFECTIVELY ORGANIZED TRIBUTARIES 2) (Protein MERISTEM-DEFECTIVE) |
| Scaffold_672 | 30354 | A | G | 11 | 313.78 | exon | Transition | 1/1 | Scarecrow-like protein 15 (AtSCL15) (GRAS family protein 25) (AtGRAS-25) |
| Scaffold_141 | 176384 | A | G | 13 | 58.77 | exon | Transition | 0/1 | Scarecrow-like protein 33 (AtSCL33) (GRAS family protein 12) (AtGRAS-12) |
| Scaffold_770 | 35240 | C | T | 17 | 177.77 | exon | Transition | 0/1 | Scopoletin glucosyltransferase (EC 2.4.1.128) (Phenylpropanoid:glucosyltransferase 1) |
| Scaffold_770 | 35244 | T | C | 13 | 95.77 | exon | Transition | 0/1 | Scopoletin glucosyltransferase (EC 2.4.1.128) (Phenylpropanoid:glucosyltransferase 1) |
| Scaffold_770 | 37451 | C | T | 10 | 103.77 | intron | Transition | 0/1 | Scopoletin glucosyltransferase (EC 2.4.1.128) (Phenylpropanoid:glucosyltransferase 1) |
| Scaffold_599 | 37957 | C | T | 56 | 62.77 | exon | Transition | 0/1 | Seed trypsin/chymotrypsin inhibitor TI5-72 |
| Scaffold_599 | 37990 | A | G | 25 | 716.77 | exon | Transition | 0/1 | Seed trypsin/chymotrypsin inhibitor TI5-72 |
| Scaffold_599 | 38000 | G | A | 10 | 259.18 | exon | Transition | 0/1 | Seed trypsin/chymotrypsin inhibitor TI5-72 |
| Scaffold_111 | 293102 | T | C | 87 | 2044.77 | CDS | Transition | 0/1 | Serine decarboxylase (AtSDC) (EC 4.1.1.-) (Protein EMBRYO DEFECTIVE 1075) (Serine decarboxylase 1) (AtSDC1) |
| Scaffold_146 | 198816 | A | G | 27 | 55.77 | CDS | Transition | 0/1 | Serine hydroxymethyltransferase 2, mitochondrial (SHMT2) (EC 2.1.2.1) (Glycine hydroxymethyltransferase 2) (Serine methylase 2) |
| Scaffold_615 | 2182 | G | A | 30 | 167.77 | CDS | Transition | 0/1 | Serine/threonine-protein kinase BSK6 (EC 2.7.11.1) (Brassinosteroid-signaling kinase 6) |
| Scaffold_3937 | 15820 | C | T | 72 | 2077.77 | exon | Transition | 1/1 | Serine/threonine-protein phosphatase PP1 isozyme 4 (EC 3.1.3.16) (Type one protein phosphatase 4) |
| Scaffold_165 | 47391 | T | C | 12 | 341.78 | CDS | Transition | 1/1 | Solute carrier family 40 member 3, chloroplastic (Ferroportin-3) (Iron-regulated transporter 3) (AtIREG3) (Protein MULTIPLE ANTIBIOTIC RESISTANCE 1) |
| Scaffold_141 | 299298 | C | T | 12 | 153.77 | noncoding | Transition | 0/1 | Soyasaponin III rhamnosyltransferase (EC 2.4.1.273) (Soyasaponin glycosyltransferase 3) (UDP-rhamnose:soyasaponin III-rhamnosyltransferase) |
| Scaffold_141 | 299956 | G | A | 30 | 98.77 | CDS | Transition | 0/1 | Soyasaponin III rhamnosyltransferase (EC 2.4.1.273) (Soyasaponin glycosyltransferase 3) (UDP-rhamnose:soyasaponin III-rhamnosyltransferase) |