Search for Variation information by Variation ID:
Detailed information for vg1105974350:
| Variant ID: vg1105974350 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974350 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTGATAGCCACCCATTTTATTATTGCCGAAATCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGC[A/G]
GCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACAT
Reverse complement sequence
ATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGC[T/C]
GCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGATTTCGGCAATAATAAAATGGGTGGCTATCAA
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974350 | A -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:20.775; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
| vg1105974350 | A -> G | LOC_Os11g10840.1 | missense_variant ; p.Ser11Gly; MODERATE | nonsynonymous_codon ; S11G | Average:20.775; most accessible tissue: Callus, score: 34.526 | benign  |
1.071 |
TOLERATED | 0.05 |
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