| Variant ID: vg1111258237 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 11258237 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, G: 0.00, others allele: 0.00, population size: 322. )
CATGCTCTTTTTTTTAAGCACTAAAAGGAGTAATCAGCATGGCAAATTCACAACTAACATAATCAATTGACAAACAAATCATTCTTCAAGATCAGGATGC[A/G]
CATCAGTCTTGCCATCTGCAGGAAGAGGGAAAGCAGAAGAGCCAGGCATGGCTTGTGACTGTGGAGAAGCAAGCCAAGCAGTCGGTGGCAGTGAGAACCA
TGGTTCTCACTGCCACCGACTGCTTGGCTTGCTTCTCCACAGTCACAAGCCATGCCTGGCTCTTCTGCTTTCCCTCTTCCTGCAGATGGCAAGACTGATG[T/C]
GCATCCTGATCTTGAAGAATGATTTGTTTGTCAATTGATTATGTTAGTTGTGAATTTGCCATGCTGATTACTCCTTTTAGTGCTTAAAAAAAAGAGCATG
| 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 | 90.30% | 0.10% | 0.61% | 8.97% | NA |
| All Indica | 2759 | 84.30% | 0.00% | 0.98% | 14.68% | NA |
| All Japonica | 1512 | 99.10% | 0.10% | 0.00% | 0.79% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 79.50% | 0.00% | 1.85% | 18.66% | NA |
| Indica II | 465 | 99.60% | 0.00% | 0.00% | 0.43% | NA |
| Indica III | 913 | 76.20% | 0.00% | 0.99% | 22.78% | NA |
| Indica Intermediate | 786 | 88.30% | 0.10% | 0.89% | 10.69% | NA |
| Temperate Japonica | 767 | 99.30% | 0.00% | 0.00% | 0.65% | NA |
| Tropical Japonica | 504 | 98.80% | 0.40% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 87.80% | 2.20% | 2.22% | 7.78% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1111258237 | A -> DEL | LOC_Os11g19530.1 | N | frameshift_variant | Average:72.686; most accessible tissue: Zhenshan97 panicle, score: 88.062 | N | N | N | N |
| vg1111258237 | A -> G | LOC_Os11g19530.1 | missense_variant ; p.Val72Ala; MODERATE | nonsynonymous_codon ; V72A | Average:72.686; most accessible tissue: Zhenshan97 panicle, score: 88.062 | unknown | unknown | TOLERATED | 0.29 |