Search for Variation information by Variation ID:
Detailed information for vg0220869576:
| Variant ID: vg0220869576 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 20869576 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 322. )
Flanking Sequence (100 bp) in Reference Genome:
GAACTTAAGAGCTTAAGTGTCTTTCGTATTGTTTATGATTGTTTAGGCACAATTGGTTGCCAGGAGATCAAAATGAAAAAAAAAGATGGTAGTCCTCACC[T/C]
CAGGTGGATCGAACTTTGCACCAAGGTCGCTCAGTTTAGCATGAGCTTCAGCGTAGTCTTTAAAGAATGCCTCCTGATCCTCTGCATATTTTTCGGCATA
Reverse complement sequence
TATGCCGAAAAATATGCAGAGGATCAGGAGGCATTCTTTAAAGACTACGCTGAAGCTCATGCTAAACTGAGCGACCTTGGTGCAAAGTTCGATCCACCTG[A/G]
GGTGAGGACTACCATCTTTTTTTTTCATTTTGATCTCCTGGCAACCAATTGTGCCTAAACAATCATAAACAATACGAAAGACACTTAAGCTCTTAAGTTC
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0220869576 | T -> C | LOC_Os02g34810.1 | missense_variant&splice_region_variant ; p.Glu352Gly; MODERATE | nonsynonymous_codon ; E352G | Average:50.534; most accessible tissue: Zhenshan97 young leaf, score: 68.794 | possibly damaging  |
1.621 |
DELETERIOUS | 0.04 |
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