| Variant ID: vg0524150114 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 24150114 |
| 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, others allele: 0.00, population size: 304. )
AAATGTAAATTACGGCAACAAAAGTTGGATCGAGCTGAGTTGTGAATTCTTACAGGATCATGAGGTTTGACAGCCCAGCCAGCTCGTTTGGGATTGGCCC[A/G]
GTTAAAAGGTTGTGATCAATTCTCCTGCCAAGAGTAAAGAAAAAACAAAAACTCAAACATAGATATCAAAGTACATTTTGCATAGCTGAACAGTACTTTC
GAAAGTACTGTTCAGCTATGCAAAATGTACTTTGATATCTATGTTTGAGTTTTTGTTTTTTCTTTACTCTTGGCAGGAGAATTGATCACAACCTTTTAAC[T/C]
GGGCCAATCCCAAACGAGCTGGCTGGGCTGTCAAACCTCATGATCCTGTAAGAATTCACAACTCAGCTCGATCCAACTTTTGTTGCCGTAATTTACATTT
| 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 | 98.90% | 0.90% | 0.21% | 0.00% | NA |
| All Indica | 2759 | 98.20% | 1.50% | 0.36% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 97.80% | 1.30% | 0.84% | 0.00% | NA |
| Indica II | 465 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.20% | 0.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.30% | 3.10% | 0.64% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0524150114 | A -> G | LOC_Os05g41230.1 | synonymous_variant ; p.Thr157Thr; LOW | N | Average:71.128; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0524150114 | A -> G | LOC_Os05g41240.1 | downstream_gene_variant ; 3619.0bp to feature; MODIFIER | N | Average:71.128; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0524150114 | A -> G | LOC_Os05g41240.3 | downstream_gene_variant ; 3619.0bp to feature; MODIFIER | N | Average:71.128; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |
| vg0524150114 | A -> G | LOC_Os05g41240.2 | downstream_gene_variant ; 3619.0bp to feature; MODIFIER | N | Average:71.128; most accessible tissue: Minghui63 panicle, score: 86.85 | N | N | N | N |