Search for Variation information by Variation ID:
Detailed information for vg0136521829:
| Variant ID: vg0136521829 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36521829 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGCCGTACAAAAATAAACGAATACTAACCTGCTGCTTTGGATGAAATCCACTGCTATGGCCCATCGATTTTGCCATTGTTGCCCCGCTCCTGCATTCAG[C/T]
CGACTCTAGATCGATTACTTCTGCTTCAGGAACACATGTTGTTGAGAGAGGATCCATCGCTGGAGGAAGGGGAGGAGTCATCACTGGAGGAAGGAACAAA
Reverse complement sequence
TTTGTTCCTTCCTCCAGTGATGACTCCTCCCCTTCCTCCAGCGATGGATCCTCTCTCAACAACATGTGTTCCTGAAGCAGAAGTAATCGATCTAGAGTCG[G/A]
CTGAATGCAGGAGCGGGGCAACAATGGCAAAATCGATGGGCCATAGCAGTGGATTTCATCCAAAGCAGCAGGTTAGTATTCGTTTATTTTTGTACGGCAA
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136521829 | C -> T | LOC_Os01g63040.1 | missense_variant ; p.Ala20Thr; MODERATE | nonsynonymous_codon ; A20T | Average:4.799; most accessible tissue: Callus, score: 8.115 | benign  |
1.282 |
TOLERATED | 0.06 |
| vg0136521829 | C -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.799; most accessible tissue: Callus, score: 8.115 | N | N | N | N |
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