| Variant ID: vg0811251553 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 11251553 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 126. )
TAGCATCAATTTAAATTATACATTTCATCAATTTATGATACTTGCTTCCAATTGAACATGCTATGTCAAGTTAACCAACAACATATCAACACAAGTAGTC[T/C]
GACTCATGGTGAGCATGCTCACAAACACCAATATCATACCCGCTAGATAAATATGTCAGACAAACTTCATCAACAATAGCCTTTTTACAACAAAAGGTCA
TGACCTTTTGTTGTAAAAAGGCTATTGTTGATGAAGTTTGTCTGACATATTTATCTAGCGGGTATGATATTGGTGTTTGTGAGCATGCTCACCATGAGTC[A/G]
GACTACTTGTGTTGATATGTTGTTGGTTAACTTGACATAGCATGTTCAATTGGAAGCAAGTATCATAAATTGATGAAATGTATAATTTAAATTGATGCTA
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.00% | 5.50% | 3.51% | 0.00% | NA |
| All Indica | 2759 | 84.80% | 9.40% | 5.80% | 0.00% | NA |
| All Japonica | 1512 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| Aus | 269 | 99.30% | 0.00% | 0.74% | 0.00% | NA |
| Indica I | 595 | 75.10% | 10.60% | 14.29% | 0.00% | NA |
| Indica II | 465 | 91.60% | 3.90% | 4.52% | 0.00% | NA |
| Indica III | 913 | 84.60% | 14.20% | 1.20% | 0.00% | NA |
| Indica Intermediate | 786 | 88.40% | 6.10% | 5.47% | 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 | 99.60% | 0.40% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 95.60% | 1.10% | 3.33% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0811251553 | T -> C | LOC_Os08g18850.1 | synonymous_variant ; p.Ser83Ser; LOW | synonymous_codon | Average:15.984; most accessible tissue: Zhenshan97 panicle, score: 24.575 | N | N | N | N |