| Variant ID: vg0823070595 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 23070595 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, T: 0.02, others allele: 0.00, population size: 241. )
GCCTTCCGGATTAAGATATCCAATAATAAAAAGGATTCATCGATCAAGTATTGACGTTTCGAAACGACAAAAGAGAATAAGAGGAAATGCACCACAGATG[T/A]
ATTTGAAATCGACGCTTGCATGCTCAATCAGGCACTCAAAGCATATGCTCAGAGAAAAATACACTACAAATGAATTTGAAGTCGACACTTGCATGCTCTA
TAGAGCATGCAAGTGTCGACTTCAAATTCATTTGTAGTGTATTTTTCTCTGAGCATATGCTTTGAGTGCCTGATTGAGCATGCAAGCGTCGATTTCAAAT[A/T]
CATCTGTGGTGCATTTCCTCTTATTCTCTTTTGTCGTTTCGAAACGTCAATACTTGATCGATGAATCCTTTTTATTATTGGATATCTTAATCCGGAAGGC
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 66.60% | 33.10% | 0.04% | 0.32% | NA |
| All Indica | 2759 | 98.50% | 0.90% | 0.04% | 0.51% | NA |
| All Japonica | 1512 | 1.50% | 98.40% | 0.00% | 0.07% | NA |
| Aus | 269 | 96.70% | 3.30% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.50% | 0.00% | 0.00% | 0.50% | NA |
| Indica II | 465 | 97.60% | 1.10% | 0.22% | 1.08% | NA |
| Indica III | 913 | 99.30% | 0.40% | 0.00% | 0.22% | NA |
| Indica Intermediate | 786 | 97.30% | 2.20% | 0.00% | 0.51% | NA |
| Temperate Japonica | 767 | 1.70% | 98.20% | 0.00% | 0.13% | NA |
| Tropical Japonica | 504 | 0.80% | 99.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 2.50% | 97.50% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 92.70% | 7.30% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 62.20% | 36.70% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0823070595 | T -> A | LOC_Os08g36540.1 | 3_prime_UTR_variant ; 169.0bp to feature; MODIFIER | silent_mutation | Average:49.37; most accessible tissue: Minghui63 root, score: 72.134 | N | N | N | N |
| vg0823070595 | T -> A | LOC_Os08g36530.1 | downstream_gene_variant ; 3615.0bp to feature; MODIFIER | silent_mutation | Average:49.37; most accessible tissue: Minghui63 root, score: 72.134 | N | N | N | N |
| vg0823070595 | T -> A | LOC_Os08g36550.1 | downstream_gene_variant ; 1568.0bp to feature; MODIFIER | silent_mutation | Average:49.37; most accessible tissue: Minghui63 root, score: 72.134 | N | N | N | N |
| vg0823070595 | T -> DEL | N | N | silent_mutation | Average:49.37; most accessible tissue: Minghui63 root, score: 72.134 | N | N | N | N |