| Variant ID: vg1126903372 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903372 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 36. )
TTTTATGTTTGGTTAAAGGGTAGGGTGGATGGGGCGGCCCGGAATAGAAAATATTCTCTTAATAGGCTGGACGACGAGTGATGTCCATGTGGCTGATAAC[G/A]
GGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGGCCATCACCAACCTGTACATGGCGCTATTGTCCT
AGGACAATAGCGCCATGTACAGGTTGGTGATGGCCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCC[C/T]
GTTATCAGCCACATGGACATCACTCGTCGTCCAGCCTATTAAGAGAATATTTTCTATTCCGGGCCGCCCCATCCACCCTACCCTTTAACCAAACATAAAA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 48.40% | 16.80% | 3.72% | 31.06% | NA |
| All Indica | 2759 | 49.00% | 8.00% | 3.23% | 39.69% | NA |
| All Japonica | 1512 | 41.30% | 36.30% | 3.90% | 18.45% | NA |
| Aus | 269 | 68.40% | 4.50% | 7.81% | 19.33% | NA |
| Indica I | 595 | 35.30% | 13.80% | 4.03% | 46.89% | NA |
| Indica II | 465 | 62.40% | 3.70% | 0.43% | 33.55% | NA |
| Indica III | 913 | 51.80% | 2.40% | 4.16% | 41.62% | NA |
| Indica Intermediate | 786 | 48.30% | 12.80% | 3.18% | 35.62% | NA |
| Temperate Japonica | 767 | 19.80% | 63.40% | 2.48% | 14.34% | NA |
| Tropical Japonica | 504 | 68.80% | 3.20% | 6.35% | 21.63% | NA |
| Japonica Intermediate | 241 | 52.30% | 19.50% | 3.32% | 24.90% | NA |
| VI/Aromatic | 96 | 85.40% | 0.00% | 2.08% | 12.50% | NA |
| Intermediate | 90 | 48.90% | 12.20% | 5.56% | 33.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903372 | G -> A | LOC_Os11g44460.1 | synonymous_variant ; p.Pro101Pro; LOW | synonymous_codon | Average:13.254; most accessible tissue: Callus, score: 46.436 | N | N | N | N |
| vg1126903372 | G -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:13.254; most accessible tissue: Callus, score: 46.436 | N | N | N | N |