| Variant ID: vg0521668157 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 21668157 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )
GCATTTTGTCTCTCGCCTGTTCAATCACACCAAAAGTTGATAAGTATATTTTGTTGGATTTTATTGTTCCTGGCAATGATTCAATTGCTCTTGTCAAAAA[T/A]
TGCATCAACAATTAATTCAACAAACGCTACAATTTGATTTTCAGCAGGCTTTTATTAGTTTCCGTTATCATTAAAAAATTGTGTCTTTGAGCTGCCAACT
AGTTGGCAGCTCAAAGACACAATTTTTTAATGATAACGGAAACTAATAAAAGCCTGCTGAAAATCAAATTGTAGCGTTTGTTGAATTAATTGTTGATGCA[A/T]
TTTTTGACAAGAGCAATTGAATCATTGCCAGGAACAATAAAATCCAACAAAATATACTTATCAACTTTTGGTGTGATTGAACAGGCGAGAGACAAAATGC
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.50% | 1.50% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 73.60% | 26.40% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.70% | 0.30% | 0.00% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0521668157 | T -> A | LOC_Os05g37080.1 | 3_prime_UTR_variant ; 247.0bp to feature; MODIFIER | silent_mutation | Average:51.694; most accessible tissue: Zhenshan97 root, score: 72.188 | N | N | N | N |
| vg0521668157 | T -> A | LOC_Os05g37070.1 | upstream_gene_variant ; 2586.0bp to feature; MODIFIER | silent_mutation | Average:51.694; most accessible tissue: Zhenshan97 root, score: 72.188 | N | N | N | N |