Search for Variation information by Variation ID:
Detailed information for vg1105974420:
| Variant ID: vg1105974420 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5974420 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
ATGGTGCTGGAGGCCGGCGAGCACCGCGGCAGCTCGGTGACGGCGAAGGGCCGCATCGACATGGACGCCGGGGAGCGCGAGTCGGTGGTGATCGGCGGCA[C/T]
GGGGCGGTTTCGGCTCGCGCGCGGGTACATGGTCACCAAGAACTACGACTACAGCCTCGCCACCGGCGGCGTCGTCCAGATCGACGTCTGCCTGCAGCAC
Reverse complement sequence
GTGCTGCAGGCAGACGTCGATCTGGACGACGCCGCCGGTGGCGAGGCTGTAGTCGTAGTTCTTGGTGACCATGTACCCGCGCGCGAGCCGAAACCGCCCC[G/A]
TGCCGCCGATCACCACCGACTCGCGCTCCCCGGCGTCCATGTCGATGCGGCCCTTCGCCGTCACCGAGCTGCCGCGGTGCTCGCCGGCCTCCAGCACCAT
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105974420 | C -> T | LOC_Os11g10840.1 | missense_variant ; p.Thr34Met; MODERATE | nonsynonymous_codon ; T34M | Average:29.982; most accessible tissue: Minghui63 root, score: 40.262 | probably damaging  |
2.863 |
DELETERIOUS | 0.00 |
| vg1105974420 | C -> DEL | LOC_Os11g10840.1 | N | frameshift_variant | Average:29.982; most accessible tissue: Minghui63 root, score: 40.262 | N | N | N | N |
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