Search for Variation information by Variation ID:
Detailed information for vg0903406052:
| Variant ID: vg0903406052 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 3406052 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 291. )
Flanking Sequence (100 bp) in Reference Genome:
GCGCTGCTCTTCTGGAATATCAGTTGATACAGGATAACCGATCAGCCTGCAAACCCAAAAAGGATCTCCTGCGGTTGTACCTTCAAAAGCATCAACTGGC[G/A]
CACCCAACGCCAAGGCTATACCTCGCATGATCTTTCTTGAAAGATCTACAAGTAAATTTTCATAACAAATGCTGTCACTCATAAGTAACAAATAATAAAT
Reverse complement sequence
ATTTATTATTTGTTACTTATGAGTGACAGCATTTGTTATGAAAATTTACTTGTAGATCTTTCAAGAAAGATCATGCGAGGTATAGCCTTGGCGTTGGGTG[C/T]
GCCAGTTGATGCTTTTGAAGGTACAACCGCAGGAGATCCTTTTTGGGTTTGCAGGCTGATCGGTTATCCTGTATCAACTGATATTCCAGAAGAGCAGCGC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.90% | 0.20% | 0.85% | 0.00% | NA |
| All Indica | 2759 | 99.90% | 0.00% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 96.90% | 0.60% | 2.51% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 99.80% | 0.20% | 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 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 94.30% | 1.20% | 4.56% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 0.00% | 1.24% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 0.00% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0903406052 | G -> A | LOC_Os09g07020.1 | missense_variant ; p.Ala276Val; MODERATE | nonsynonymous_codon ; A276V | Average:50.656; most accessible tissue: Zhenshan97 young leaf, score: 72.34 | possibly damaging  |
1.583 |
TOLERATED | 0.46 |
| vg0903406052 | G -> A | LOC_Os09g07020.2 | missense_variant ; p.Ala275Val; MODERATE | nonsynonymous_codon ; A275V | Average:50.656; most accessible tissue: Zhenshan97 young leaf, score: 72.34 | possibly damaging |
1.583 |
TOLERATED | 0.21 |