Search for Variation information by Variation ID:
Detailed information for vg0136520357:
| Variant ID: vg0136520357 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 36520357 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 318. )
Flanking Sequence (100 bp) in Reference Genome:
AGGTGTGAAAAGTTTGGTATCTCAAATATTTCGCACAATATTTGTTTCTTCCCATCCAATTCATCTTGAGAGCAAGGGATAATAGGTTGACCTGAGCATG[G/A]
CAAGCCAAAAACTGCATTCACATCATTAGGACCGAATGGCAACTCCTGGTTGACATCTTTAACAATAGCGCATGATTTCGGATCAACTTTGCTCAGTAGC
Reverse complement sequence
GCTACTGAGCAAAGTTGATCCGAAATCATGCGCTATTGTTAAAGATGTCAACCAGGAGTTGCCATTCGGTCCTAATGATGTGAATGCAGTTTTTGGCTTG[C/T]
CATGCTCAGGTCAACCTATTATCCCTTGCTCTCAAGATGAATTGGATGGGAAGAAACAAATATTGTGCGAAATATTTGAGATACCAAACTTTTCACACCT
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0136520357 | G -> A | LOC_Os01g63040.1 | missense_variant ; p.Pro178Ser; MODERATE | nonsynonymous_codon ; P178S | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | possibly damaging  |
1.531 |
DELETERIOUS | 0.00 |
| vg0136520357 | G -> DEL | LOC_Os01g63040.1 | N | frameshift_variant | Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |
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