Search for Variation information by Variation ID:
Detailed information for vg0421623894:
| Variant ID: vg0421623894 (JBrowse) | Variation Type: SNP |
| Chromosome: chr04 | Position: 21623894 |
| Reference Allele: T | Alternative Allele: C,G |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 350. )
Flanking Sequence (100 bp) in Reference Genome:
GGGAAGTGAGAGTACAGTTTAAGCATTATTCACCTTGAATGTTGGGTCCTCAAATAATGCAGCATCTGTAGGCAAGACCAGGAGATCCTGATCTCTTTTC[T/C,G]
CTTTTATCTCCTGCAGTATTGCCACCAGGCACCAGCTCACATCATGCAAAATCATATGAATCATCCGACATGAAGAATAAGGGAAAAGTGGCACGTACCT
Reverse complement sequence
AGGTACGTGCCACTTTTCCCTTATTCTTCATGTCGGATGATTCATATGATTTTGCATGATGTGAGCTGGTGCCTGGTGGCAATACTGCAGGAGATAAAAG[A/G,C]
GAAAAGAGATCAGGATCTCCTGGTCTTGCCTACAGATGCTGCATTATTTGAGGACCCAACATTCAAGGTGAATAATGCTTAAACTGTACTCTCACTTCCC
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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0421623894 | T -> C | LOC_Os04g35520.1 | missense_variant ; p.Glu296Gly; MODERATE | nonsynonymous_codon ; E296G | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign  |
0.83 |
TOLERATED | 0.07 |
| vg0421623894 | T -> C | LOC_Os04g35520.2 | missense_variant ; p.Glu296Gly; MODERATE | nonsynonymous_codon ; E296G | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.83 |
TOLERATED | 0.07 |
| vg0421623894 | T -> C | LOC_Os04g35520.3 | missense_variant ; p.Glu296Gly; MODERATE | nonsynonymous_codon ; E296G | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.83 |
TOLERATED | 0.07 |
| vg0421623894 | T -> C | LOC_Os04g35520.4 | missense_variant ; p.Glu295Gly; MODERATE | nonsynonymous_codon ; E295G | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.83 |
TOLERATED | 0.07 |
| vg0421623894 | T -> G | LOC_Os04g35520.1 | missense_variant ; p.Glu296Ala; MODERATE | nonsynonymous_codon ; E296A | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.427 |
TOLERATED | 0.14 |
| vg0421623894 | T -> G | LOC_Os04g35520.2 | missense_variant ; p.Glu296Ala; MODERATE | nonsynonymous_codon ; E296A | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.427 |
TOLERATED | 0.14 |
| vg0421623894 | T -> G | LOC_Os04g35520.3 | missense_variant ; p.Glu296Ala; MODERATE | nonsynonymous_codon ; E296A | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.427 |
TOLERATED | 0.14 |
| vg0421623894 | T -> G | LOC_Os04g35520.4 | missense_variant ; p.Glu295Ala; MODERATE | nonsynonymous_codon ; E295A | Average:60.015; most accessible tissue: Minghui63 flower, score: 72.615 | benign |
0.427 |
TOLERATED | 0.14 |
Showing 1 to 8 of 8 entries