Search for Variation information by Variation ID:
Detailed information for vg1126362807:
| Variant ID: vg1126362807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26362807 |
| 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, others allele: 0.00, population size: 232. )
Flanking Sequence (100 bp) in Reference Genome:
TCGGTCCATTCCGGCGACGAGGGTCACGTCCTCGCCGTCGAGGGCGCTCCGCGGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAAGAGGCTG[G/A]
TACTCCCAGCAGGGAGCGCCCAGCCAGCAAGTGGTGCTCCGTCCACAACACCTCCCTCCACGATCTTGCGGACTGTCGCGCAGTCAAAAACTTGGCTGAG
Reverse complement sequence
CTCAGCCAAGTTTTTGACTGCGCGACAGTCCGCAAGATCGTGGAGGGAGGTGTTGTGGACGGAGCACCACTTGCTGGCTGGGCGCTCCCTGCTGGGAGTA[C/T]
CAGCCTCTTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCCGCGGAGCGCCCTCGACGGCGAGGACGTGACCCTCGTCGCCGGAATGGACCGA
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 | 7.70% | 0.10% | 11.24% | 80.96% | NA |
| All Indica | 2759 | 2.90% | 0.10% | 8.41% | 88.58% | NA |
| All Japonica | 1512 | 17.90% | 0.00% | 13.82% | 68.32% | NA |
| Aus | 269 | 1.10% | 0.70% | 23.42% | 74.72% | NA |
| Indica I | 595 | 1.20% | 0.20% | 3.36% | 95.29% | NA |
| Indica II | 465 | 2.60% | 0.00% | 2.37% | 95.05% | NA |
| Indica III | 913 | 3.30% | 0.20% | 15.22% | 81.27% | NA |
| Indica Intermediate | 786 | 3.80% | 0.10% | 7.89% | 88.17% | NA |
| Temperate Japonica | 767 | 30.80% | 0.00% | 4.56% | 64.67% | NA |
| Tropical Japonica | 504 | 1.00% | 0.00% | 26.19% | 72.82% | NA |
| Japonica Intermediate | 241 | 12.00% | 0.00% | 17.43% | 70.54% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 15.62% | 83.33% | NA |
| Intermediate | 90 | 11.10% | 0.00% | 13.33% | 75.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126362807 | G -> A | LOC_Os11g43670.1 | missense_variant ; p.Gly463Asp; MODERATE | nonsynonymous_codon ; G463D | Average:12.875; most accessible tissue: Minghui63 panicle, score: 20.733 | probably damaging  |
2.173 |
DELETERIOUS | 0.01 |
| vg1126362807 | G -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:12.875; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |