| Variant ID: vg1213095455 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 13095455 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 318. )
TAGGGCAAGCAGCAGAAGCTCTAAAATGGATCAGTAGTTGTCGAGGCAAGAAGACAACGATTTCAACCATCAGAATAAAAAAGGGCAGCCTCAAACTCCA[C/T]
TCCTGACTTGGCCATGTCCAAAATCAATGTATAAAGGAAAATGGTACACATCGGCCTTCTTTTTGCGGATTGAAGATCAACAGGAGTAGCGCAACATACA
TGTATGTTGCGCTACTCCTGTTGATCTTCAATCCGCAAAAAGAAGGCCGATGTGTACCATTTTCCTTTATACATTGATTTTGGACATGGCCAAGTCAGGA[G/A]
TGGAGTTTGAGGCTGCCCTTTTTTATTCTGATGGTTGAAATCGTTGTCTTCTTGCCTCGACAACTACTGATCCATTTTAGAGCTTCTGCTGCTTGCCCTA
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.80% | 0.00% | 0.44% | 10.77% | NA |
| All Indica | 2759 | 82.20% | 0.00% | 0.72% | 17.07% | NA |
| All Japonica | 1512 | 97.60% | 0.00% | 0.07% | 2.31% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.80% | 0.00% | 0.17% | 1.01% | NA |
| Indica II | 465 | 60.90% | 0.00% | 1.94% | 37.20% | NA |
| Indica III | 913 | 81.80% | 0.10% | 0.66% | 17.42% | NA |
| Indica Intermediate | 786 | 82.60% | 0.00% | 0.51% | 16.92% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 99.60% | 0.00% | 0.00% | 0.40% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.00% | 0.83% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 96.70% | 0.00% | 0.00% | 3.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1213095455 | C -> DEL | LOC_Os12g23150.1 | N | frameshift_variant | Average:66.366; most accessible tissue: Minghui63 flower, score: 81.118 | N | N | N | N |
| vg1213095455 | C -> T | LOC_Os12g23150.1 | missense_variant ; p.Val224Met; MODERATE | nonsynonymous_codon ; V224I | Average:66.366; most accessible tissue: Minghui63 flower, score: 81.118 | unknown | unknown | DELETERIOUS | 0.00 |