Search for Variation information by Variation ID:
Detailed information for vg1126362815:
| Variant ID: vg1126362815 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26362815 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 222. )
Flanking Sequence (100 bp) in Reference Genome:
TTCCGGCGACGAGGGTCACGTCCTCGCCGTCGAGGGCGCTCCGCGGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAAGAGGCTGGTACTCCC[A/G]
GCAGGGAGCGCCCAGCCAGCAAGTGGTGCTCCGTCCACAACACCTCCCTCCACGATCTTGCGGACTGTCGCGCAGTCAAAAACTTGGCTGAGCGAACGAG
Reverse complement sequence
CTCGTTCGCTCAGCCAAGTTTTTGACTGCGCGACAGTCCGCAAGATCGTGGAGGGAGGTGTTGTGGACGGAGCACCACTTGCTGGCTGGGCGCTCCCTGC[T/C]
GGGAGTACCAGCCTCTTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCCGCGGAGCGCCCTCGACGGCGAGGACGTGACCCTCGTCGCCGGAA
Allele Frequencies:
| 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 | 12.40% | 0.10% | 26.64% | 60.85% | NA |
| All Indica | 2759 | 5.90% | 0.10% | 23.02% | 70.93% | NA |
| All Japonica | 1512 | 22.90% | 0.00% | 30.49% | 46.56% | NA |
| Aus | 269 | 21.60% | 0.70% | 37.17% | 40.52% | NA |
| Indica I | 595 | 3.70% | 0.20% | 10.25% | 85.88% | NA |
| Indica II | 465 | 4.70% | 0.00% | 12.04% | 83.23% | NA |
| Indica III | 913 | 6.40% | 0.20% | 37.46% | 55.97% | NA |
| Indica Intermediate | 786 | 7.80% | 0.10% | 22.39% | 69.72% | NA |
| Temperate Japonica | 767 | 38.50% | 0.00% | 7.69% | 53.85% | NA |
| Tropical Japonica | 504 | 2.40% | 0.00% | 60.32% | 37.30% | NA |
| Japonica Intermediate | 241 | 16.60% | 0.00% | 40.66% | 42.74% | NA |
| VI/Aromatic | 96 | 2.10% | 0.00% | 42.71% | 55.21% | NA |
| Intermediate | 90 | 16.70% | 0.00% | 24.44% | 58.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126362815 | A -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:13.016; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1126362815 | A -> G | LOC_Os11g43670.1 | missense_variant ; p.Ser466Gly; MODERATE | nonsynonymous_codon ; S466G | Average:13.016; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
0.269 |
DELETERIOUS | 0.04 |