| Variant ID: vg0522745124 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 22745124 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.95, G: 0.04, others allele: 0.00, population size: 245. )
TGGCAACAAATTATAAGCCCAAGATTTGCACGTGTATAGTAGATTTGCATGTGATAAATTGGGTGTATCCAATTGATGATCAGAGTGTACAAAGCCATAC[G/A]
TTTTAAACCATTTAGCATGTTCGTTATTATCACAACAAAAAACATTTACTTGTTGAAGCCCCACCCCCCAATTTACATTGTCCACGGCCTCTGAGAAACG
CGTTTCTCAGAGGCCGTGGACAATGTAAATTGGGGGGTGGGGCTTCAACAAGTAAATGTTTTTTGTTGTGATAATAACGAACATGCTAAATGGTTTAAAA[C/T]
GTATGGCTTTGTACACTCTGATCATCAATTGGATACACCCAATTTATCACATGCAAATCTACTATACACGTGCAAATCTTGGGCTTATAATTTGTTGCCA
| 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 | 66.30% | 33.60% | 0.08% | 0.02% | NA |
| All Indica | 2759 | 99.20% | 0.70% | 0.11% | 0.04% | NA |
| All Japonica | 1512 | 3.80% | 96.20% | 0.00% | 0.00% | NA |
| Aus | 269 | 97.80% | 2.20% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.30% | 0.00% | 0.17% | NA |
| Indica II | 465 | 99.10% | 0.90% | 0.00% | 0.00% | NA |
| Indica III | 913 | 99.70% | 0.20% | 0.11% | 0.00% | NA |
| Indica Intermediate | 786 | 98.30% | 1.40% | 0.25% | 0.00% | NA |
| Temperate Japonica | 767 | 0.50% | 99.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 9.10% | 90.90% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.90% | 97.10% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 26.00% | 74.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 60.00% | 38.90% | 1.11% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0522745124 | G -> DEL | N | N | silent_mutation | Average:34.144; most accessible tissue: Zhenshan97 young leaf, score: 52.657 | N | N | N | N |
| vg0522745124 | G -> A | LOC_Os05g38770.1 | 3_prime_UTR_variant ; 241.0bp to feature; MODIFIER | silent_mutation | Average:34.144; most accessible tissue: Zhenshan97 young leaf, score: 52.657 | N | N | N | N |
| vg0522745124 | G -> A | LOC_Os05g38760.1 | upstream_gene_variant ; 672.0bp to feature; MODIFIER | silent_mutation | Average:34.144; most accessible tissue: Zhenshan97 young leaf, score: 52.657 | N | N | N | N |