Search for Variation information by Variation ID:
Detailed information for vg0203127408:
| Variant ID: vg0203127408 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3127408 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
GAGTTGTCAAATGTATCAAACTGGCCTCCAGTTGGAATAGGTCCTTCCAGGTCATTGTTAGAAACATTGAAGGCAGAAAGGAAGTGCAGCTTGTTCAGTT[C/T]
CAAAGGGATTGCACCCATTAGATTGTTGCTAGACAAGTCTAGCATCTCCAGGTTGGTGAGGTTGCAAATTGCTTGTGGGATCTCTCCAGAGAAGCTATTG
Reverse complement sequence
CAATAGCTTCTCTGGAGAGATCCCACAAGCAATTTGCAACCTCACCAACCTGGAGATGCTAGACTTGTCTAGCAACAATCTAATGGGTGCAATCCCTTTG[G/A]
AACTGAACAAGCTGCACTTCCTTTCTGCCTTCAATGTTTCTAACAATGACCTGGAAGGACCTATTCCAACTGGAGGCCAGTTTGATACATTTGACAACTC
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0203127408 | C -> T | LOC_Os02g06260.1 | missense_variant ; p.Glu617Lys; MODERATE | nonsynonymous_codon ; E617K | Average:48.153; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | benign  |
1.078 |
DELETERIOUS | 0.01 |
| vg0203127408 | C -> DEL | LOC_Os02g06260.1 | N | frameshift_variant | Average:48.153; most accessible tissue: Zhenshan97 young leaf, score: 59.009 | N | N | N | N |
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