Search for Variation information by Variation ID:
Detailed information for vg0431565369:
| Variant ID: vg0431565369 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 31565369 |
| Reference Allele: A | Alternative Allele: G,C |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 89. )
Flanking Sequence (100 bp) in Reference Genome:
ATCTAATATCATCCATTCTCTAAGAGAGCTAGTTATTTCTAACTGTCCTGATCTGGAGTTCGGTGGAGAAGAGGGAGCCCTCCGAGGATACACCTCTCTT[A/G,C]
AGTCCATTAAAGTTCAGGGTTGCCCCAAACTGATACCGTTGTTGGTGAGTGGTAAGATGGAGGTTGGATTGCTGCCACCGTCTCTAGAATGCTTATGTAT
Reverse complement sequence
ATACATAAGCATTCTAGAGACGGTGGCAGCAATCCAACCTCCATCTTACCACTCACCAACAACGGTATCAGTTTGGGGCAACCCTGAACTTTAATGGACT[T/C,G]
AAGAGAGGTGTATCCTCGGAGGGCTCCCTCTTCTCCACCGAACTCCAGATCAGGACAGTTAGAAATAACTAGCTCTCTTAGAGAATGGATGATATTAGAT
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0431565369 | A -> C | LOC_Os04g53000.1 | missense_variant ; p.Lys76Gln; MODERATE | nonsynonymous_codon ; K76Q | Average:53.838; most accessible tissue: Callus, score: 73.976 | benign  |
1.314 |
TOLERATED | 0.15 |
| vg0431565369 | A -> G | LOC_Os04g53000.1 | missense_variant ; p.Lys76Glu; MODERATE | nonsynonymous_codon ; K76E | Average:53.838; most accessible tissue: Callus, score: 73.976 | benign |
-0.011 |
TOLERATED | 0.99 |
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