Search for Variation information by Variation ID:
Detailed information for vg0420807529:
| Variant ID: vg0420807529 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 20807529 |
| Reference Allele: A | Alternative Allele: T,G |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.82, A: 0.18, others allele: 0.00, population size: 88. )
Flanking Sequence (100 bp) in Reference Genome:
CCAGCGAGAGAAAGACCAGAAACAAAGTAATCAGATTCTGCAAGGTTCAGTGGAGTCATCACTCAGAAGAAGAGGCCACTTGGGAAAGAGAAGATGAGTT[A/T,G]
AAGGCCACCCACCCGCACCTCTTCGCCAGCTCTTCCGAATCTCGAGGTCGAGATTCCGTTTAAGGGGGGTAGGTTTGTCACACCCTGAAGTTTCCCCCCT
Reverse complement sequence
AGGGGGGAAACTTCAGGGTGTGACAAACCTACCCCCCTTAAACGGAATCTCGACCTCGAGATTCGGAAGAGCTGGCGAAGAGGTGCGGGTGGGTGGCCTT[T/A,C]
AACTCATCTTCTCTTTCCCAAGTGGCCTCTTCTTCTGAGTGATGACTCCACTGAACCTTGCAGAATCTGATTACTTTGTTTCTGGTCTTTCTCTCGCTGG
Allele Frequencies:
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0420807529 | A -> DEL | LOC_Os04g34350.1 | N | frameshift_variant | Average:14.37; most accessible tissue: Callus, score: 23.793 | N | N | N | N |
| vg0420807529 | A -> G | LOC_Os04g34350.1 | synonymous_variant ; p.Leu1442Leu; LOW | synonymous_codon | Average:14.37; most accessible tissue: Callus, score: 23.793 | N | N | N | N |
| vg0420807529 | A -> T | LOC_Os04g34350.1 | missense_variant ; p.Leu1442Phe; MODERATE | nonsynonymous_codon ; L1442C | Average:14.37; most accessible tissue: Callus, score: 23.793 | probably damaging  |
2.629 |
DELETERIOUS | 0.00 |
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