| Variant ID: vg1100141645 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 141645 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 300. )
CTTGGTTGCCACCAGGGATTCTGTAGATCAAAAGCGCAACCTTCTTTTCAAGCGCACAAGGGATAATTGTTAACTTCTGACTCCACAGGTTAGATATCTT[G/A]
TAATTTCCTCTTAACTTTATTGTTTCTCATTTTTCTTGGAGCTTGAAGTCCTCAACCTACTACAATTTCTACTAGTAGATTACTACTGTTATATACACTA
TAGTGTATATAACAGTAGTAATCTACTAGTAGAAATTGTAGTAGGTTGAGGACTTCAAGCTCCAAGAAAAATGAGAAACAATAAAGTTAAGAGGAAATTA[C/T]
AAGATATCTAACCTGTGGAGTCAGAAGTTAACAATTATCCCTTGTGCGCTTGAAAAGAAGGTTGCGCTTTTGATCTACAGAATCCCTGGTGGCAACCAAG
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.60% | 1.10% | 0.25% | 0.00% | NA |
| All Indica | 2759 | 97.70% | 1.90% | 0.40% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.00% | 0.07% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 98.50% | 0.50% | 1.01% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 95.10% | 4.80% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.70% | 0.80% | 0.51% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.80% | 0.00% | 0.20% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1100141645 | G -> A | LOC_Os11g01250.1 | upstream_gene_variant ; 1327.0bp to feature; MODIFIER | silent_mutation | Average:52.79; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |
| vg1100141645 | G -> A | LOC_Os11g01240.1 | downstream_gene_variant ; 2686.0bp to feature; MODIFIER | silent_mutation | Average:52.79; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |
| vg1100141645 | G -> A | LOC_Os11g01270.1 | downstream_gene_variant ; 2520.0bp to feature; MODIFIER | silent_mutation | Average:52.79; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |
| vg1100141645 | G -> A | LOC_Os11g01260.1 | intron_variant ; MODIFIER | silent_mutation | Average:52.79; most accessible tissue: Zhenshan97 flower, score: 69.775 | N | N | N | N |