Search for Variation information by Variation ID:
Detailed information for vg1126362833:
| Variant ID: vg1126362833 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26362833 |
| 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: 124. )
Flanking Sequence (100 bp) in Reference Genome:
CGTCCTCGCCGTCGAGGGCGCTCCGCGGGCCACCCGAAAGGGGAGGCCTGCGAGCGACAAAAAGAAAGAGGCTGGTACTCCCAGCAGGGAGCGCCCAGCC[A/G]
GCAAGTGGTGCTCCGTCCACAACACCTCCCTCCACGATCTTGCGGACTGTCGCGCAGTCAAAAACTTGGCTGAGCGAACGAGGAAGTGGGAGGAGGACAG
Reverse complement sequence
CTGTCCTCCTCCCACTTCCTCGTTCGCTCAGCCAAGTTTTTGACTGCGCGACAGTCCGCAAGATCGTGGAGGGAGGTGTTGTGGACGGAGCACCACTTGC[T/C]
GGCTGGGCGCTCCCTGCTGGGAGTACCAGCCTCTTTCTTTTTGTCGCTCGCAGGCCTCCCCTTTCGGGTGGCCCGCGGAGCGCCCTCGACGGCGAGGACG
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 | 6.50% | 0.30% | 10.26% | 82.97% | NA |
| All Indica | 2759 | 1.20% | 0.40% | 6.16% | 92.32% | NA |
| All Japonica | 1512 | 17.50% | 0.00% | 16.80% | 65.67% | NA |
| Aus | 269 | 0.00% | 0.70% | 18.96% | 80.30% | NA |
| Indica I | 595 | 1.20% | 0.20% | 1.01% | 97.65% | NA |
| Indica II | 465 | 2.60% | 0.00% | 1.29% | 96.13% | NA |
| Indica III | 913 | 0.10% | 0.80% | 10.95% | 88.17% | NA |
| Indica Intermediate | 786 | 1.50% | 0.30% | 7.38% | 90.84% | NA |
| Temperate Japonica | 767 | 30.10% | 0.00% | 12.13% | 57.76% | NA |
| Tropical Japonica | 504 | 0.80% | 0.00% | 26.19% | 73.02% | NA |
| Japonica Intermediate | 241 | 12.40% | 0.00% | 12.03% | 75.52% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 4.17% | 95.83% | NA |
| Intermediate | 90 | 12.20% | 0.00% | 6.67% | 81.11% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126362833 | A -> DEL | LOC_Os11g43670.1 | N | frameshift_variant | Average:12.965; most accessible tissue: Minghui63 panicle, score: 20.733 | N | N | N | N |
| vg1126362833 | A -> G | LOC_Os11g43670.1 | missense_variant ; p.Ser472Gly; MODERATE | nonsynonymous_codon ; S472G | Average:12.965; most accessible tissue: Minghui63 panicle, score: 20.733 | benign  |
-0.642 |
TOLERATED | 1.00 |