Search for Variation information by Variation ID:
Detailed information for vg0509797528:
| Variant ID: vg0509797528 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 9797528 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.01, others allele: 0.00, population size: 97. )
Flanking Sequence (100 bp) in Reference Genome:
CCCTCATGATCGTGATGAAGAGAAGTGCCGGGTCAAAGTCACTTTGAACAGTAATCCTGAAGATATACCATCAGGGATGTTCGAGGCTGGAGGTGGAAGC[T/A]
ACATTCATGCTTGTCAGGAGGTGGCAAGGATCACCATAGGAGAGCTCCGCGAAAGCTACAACGATCGGTTGGCCGACACCGAGTATCGCTACCATCCTCG
Reverse complement sequence
CGAGGATGGTAGCGATACTCGGTGTCGGCCAACCGATCGTTGTAGCTTTCGCGGAGCTCTCCTATGGTGATCCTTGCCACCTCCTGACAAGCATGAATGT[A/T]
GCTTCCACCTCCAGCCTCGAACATCCCTGATGGTATATCTTCAGGATTACTGTTCAAAGTGACTTTGACCCGGCACTTCTCTTCATCACGATCATGAGGG
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0509797528 | T -> DEL | LOC_Os05g17120.1 | N | frameshift_variant | Average:48.24; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 | N | N | N | N |
| vg0509797528 | T -> A | LOC_Os05g17120.1 | missense_variant ; p.Tyr1966Asn; MODERATE | nonsynonymous_codon ; Y1966N | Average:48.24; most accessible tissue: Zhenshan97 flag leaf, score: 72.387 | probably damaging  |
2.429 |
DELETERIOUS | 0.00 |
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