Search for Variation information by Variation ID:
Detailed information for vg0431565289:
| Variant ID: vg0431565289 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 31565289 |
| Reference Allele: T | Alternative Allele: G |
| Primary Allele: T | Secondary Allele: G |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 90. )
Flanking Sequence (100 bp) in Reference Genome:
CGCGCTGCACTGTGTGTACTGCCACTTTCGATGAGATTGACTCCATCTCCGCTAGCGCTAAAACAGCTGTTGAAAATTCCATCTAATATCATCCATTCTC[T/G]
AAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTTAAGTCCATTAAAGTTCAGGGT
Reverse complement sequence
ACCCTGAACTTTAATGGACTTAAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTT[A/C]
GAGAATGGATGATATTAGATGGAATTTTCAACAGCTGTTTTAGCGCTAGCGGAGATGGAGTCAATCTCATCGAAAGTGGCAGTACACACAGTGCAGCGCG
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0431565289 | T -> DEL | LOC_Os04g53000.1 | N | frameshift_variant | Average:42.185; most accessible tissue: Callus, score: 85.988 | N | N | N | N |
| vg0431565289 | T -> G | LOC_Os04g53000.1 | missense_variant ; p.Leu49Arg; MODERATE | nonsynonymous_codon ; L49R | Average:42.185; most accessible tissue: Callus, score: 85.988 | probably damaging  |
2.363 |
DELETERIOUS | 0.04 |
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