| Variant ID: vg0410079688 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 10079688 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 119. )
GAGGACTCCAAGAGCTTTCCATCAAGTACTCACGGGCCGAAAACGGAGGTCGTATGCAGATTCGGCAGCCGTTTGAAGTCAGCAGTGTAGTAGGTGGCCG[A/T]
ATCGGATTCCAGCACTTGGAGGATTTGATCTTGATATCTTCTTGTTCATCCATGATGTGAGCAATGGTTGCATCTGTGGTAGCCATGGTCACATCATCCT
AGGATGATGTGACCATGGCTACCACAGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAATCCTCCAAGTGCTGGAATCCGAT[T/A]
CGGCCACCTACTACACTGCTGACTTCAAACGGCTGCCGAATCTGCATACGACCTCCGTTTTCGGCCCGTGAGTACTTGATGGAAAGCTCTTGGAGTCCTC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 20.90% | 4.60% | 12.10% | 62.38% | NA |
| All Indica | 2759 | 1.40% | 7.80% | 17.54% | 73.25% | NA |
| All Japonica | 1512 | 61.20% | 0.10% | 2.51% | 36.18% | NA |
| Aus | 269 | 1.10% | 0.00% | 13.01% | 85.87% | NA |
| Indica I | 595 | 0.70% | 12.40% | 18.49% | 68.40% | NA |
| Indica II | 465 | 1.70% | 12.70% | 16.56% | 69.03% | NA |
| Indica III | 913 | 1.50% | 1.40% | 17.85% | 79.19% | NA |
| Indica Intermediate | 786 | 1.80% | 8.70% | 17.05% | 72.52% | NA |
| Temperate Japonica | 767 | 95.80% | 0.00% | 0.13% | 4.04% | NA |
| Tropical Japonica | 504 | 5.60% | 0.00% | 6.15% | 88.29% | NA |
| Japonica Intermediate | 241 | 67.60% | 0.40% | 2.49% | 29.46% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 0.00% | 100.00% | NA |
| Intermediate | 90 | 22.20% | 2.20% | 16.67% | 58.89% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0410079688 | A -> DEL | LOC_Os04g18230.1 | N | frameshift_variant | Average:7.066; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |
| vg0410079688 | A -> T | LOC_Os04g18230.1 | synonymous_variant ; p.Ile29Ile; LOW | synonymous_codon | Average:7.066; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |