Search for Variation information by Variation ID:
Detailed information for vg0300021861:
| Variant ID: vg0300021861 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 21861 |
| 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: 327. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTGGGACTAGCAGATGATCTCGCAGCCAAGACGTGACCACCCAAGGCTCACATTCAGAGTTGCCAATCTTTGCATCTATGGCATTATCTTCAAGGACC[T/C]
CACACACCTATTGTATGAGAACAGGCAAAAGACAAATACAAGAAGGTCCAAAGAAGTTATGGAAAAATTAAAATGCAACAAACAAATGATTTACTACTGT
Reverse complement sequence
ACAGTAGTAAATCATTTGTTTGTTGCATTTTAATTTTTCCATAACTTCTTTGGACCTTCTTGTATTTGTCTTTTGCCTGTTCTCATACAATAGGTGTGTG[A/G]
GGTCCTTGAAGATAATGCCATAGATGCAAAGATTGGCAACTCTGAATGTGAGCCTTGGGTGGTCACGTCTTGGCTGCGAGATCATCTGCTAGTCCCACAA
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0300021861 | T -> C | LOC_Os03g01016.2 | missense_variant ; p.Glu253Gly; MODERATE | nonsynonymous_codon ; E253G | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.636 |
TOLERATED | 0.06 |
| vg0300021861 | T -> C | LOC_Os03g01016.1 | missense_variant ; p.Arg251Gly; MODERATE | nonsynonymous_codon ; R251G | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | unknown | unknown | DELETERIOUS | 0.03 |
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