Search for Variation information by Variation ID:
Detailed information for vg0223953305:
| Variant ID: vg0223953305 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 23953305 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGGAATCTGAGTTACCTTCACCTGCTTGACCTTTCTGGTAATCGCTTCTCTGGGCAGATACCTCGCCTGAACAGTCTCCGAAAATTGCAAGTCCTCAACC[T/A]
GAGTAACAATATTTTGGACGGGATCATTCCGGACACGCTTACAAACTGTTCCAGTTTGACGCAGCTAGATTTGAGCATAAACTTATTTCAAGGCCAGATT
Reverse complement sequence
AATCTGGCCTTGAAATAAGTTTATGCTCAAATCTAGCTGCGTCAAACTGGAACAGTTTGTAAGCGTGTCCGGAATGATCCCGTCCAAAATATTGTTACTC[A/T]
GGTTGAGGACTTGCAATTTTCGGAGACTGTTCAGGCGAGGTATCTGCCCAGAGAAGCGATTACCAGAAAGGTCAAGCAGGTGAAGGTAACTCAGATTCCC
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0223953305 | T -> A | LOC_Os02g39660.1 | missense_variant ; p.Leu127Gln; MODERATE | nonsynonymous_codon ; L127Q | Average:64.711; most accessible tissue: Callus, score: 79.908 | probably damaging  |
2.792 |
DELETERIOUS | 0.01 |
| vg0223953305 | T -> DEL | LOC_Os02g39660.1 | N | frameshift_variant | Average:64.711; most accessible tissue: Callus, score: 79.908 | N | N | N | N |
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