Search for Variation information by Variation ID:
Detailed information for vg1105974381:
| Variant ID: vg1105974381 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974381 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCTTTTTTCGACAGCGTGGTGTCGGACCTGAGCCTGCACATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACA[T/C]
GGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCACGGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCC
Reverse complement sequence
GGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCCGTGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCC[A/G]
TGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCATGTGCAGGCTCAGGTCCGACACCACGCTGTCGAAAAAAGA
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974381 | T -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:24.362; most accessible tissue: Callus, score: 34.526 | N | N | N | N |
| vg1105974381 | T -> C | LOC_Os11g10840.1 | missense_variant ; p.Met21Thr; MODERATE | nonsynonymous_codon ; M21T | Average:24.362; most accessible tissue: Callus, score: 34.526 | benign  |
-0.013 |
TOLERATED | 0.16 |
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