Search for Variation information by Variation ID:
Detailed information for vg0526335065:
| Variant ID: vg0526335065 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 26335065 |
| Reference Allele: T | Alternative Allele: C |
| 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: 372. )
Flanking Sequence (100 bp) in Reference Genome:
CAGACACTAACCTTGAAGGAGAAGCTTAATCTTGTTTCCCCAGGACATTTTCCATGAGCTTGAAGCAAACCACCAAAGAATGGGAAAAATCCACTTGCTG[T/C]
TATCCCTTCTCCAGCAACGTATGTTAGCTGTCCATTTGGGAACTGCACATCCATGAAAGACTGAAACAAATAGCCAAGTTAACAATGAGGGTAGAAATGA
Reverse complement sequence
TCATTTCTACCCTCATTGTTAACTTGGCTATTTGTTTCAGTCTTTCATGGATGTGCAGTTCCCAAATGGACAGCTAACATACGTTGCTGGAGAAGGGATA[A/G]
CAGCAAGTGGATTTTTCCCATTCTTTGGTGGTTTGCTTCAAGCTCATGGAAAATGTCCTGGGGAAACAAGATTAAGCTTCTCCTTCAAGGTTAGTGTCTG
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.80% | 0.20% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 95.90% | 3.70% | 0.37% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0526335065 | T -> C | LOC_Os05g45400.1 | missense_variant ; p.Thr351Ala; MODERATE | nonsynonymous_codon ; T351A | Average:52.527; most accessible tissue: Callus, score: 83.184 | benign  |
1 |
DELETERIOUS | 0.05 |