Search for Variation information by Variation ID:
Detailed information for vg0905621024:
| Variant ID: vg0905621024 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 5621024 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 309. )
Flanking Sequence (100 bp) in Reference Genome:
AAGCGAAGAGATGGATCTTCTTCCTCTGGAATAGCTGGCTCTCTTTCTTCTGGATCTTCCTCCTCTGGGGTAGCTGACGGCGGTGCTTCTCCCTTGAGCT[C/T]
GGCCAGTTCCTTCTGCAGGCGATACACCTTGCTTTCTAGCTTGCAAATCTTGCGACGGTTCCAATTTTCCCTCTCATGAGCTGCTTTCCGCCGCTCCACG
Reverse complement sequence
CGTGGAGCGGCGGAAAGCAGCTCATGAGAGGGAAAATTGGAACCGTCGCAAGATTTGCAAGCTAGAAAGCAAGGTGTATCGCCTGCAGAAGGAACTGGCC[G/A]
AGCTCAAGGGAGAAGCACCGCCGTCAGCTACCCCAGAGGAGGAAGATCCAGAAGAAAGAGAGCCAGCTATTCCAGAGGAAGAAGATCCATCTCTTCGCTT
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 82.90% | 17.10% | 0.00% | 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 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 99.60% | 0.40% | 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 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0905621024 | C -> T | LOC_Os09g10310.1 | missense_variant ; p.Glu169Lys; MODERATE | nonsynonymous_codon ; E169K | Average:54.946; most accessible tissue: Zhenshan97 flag leaf, score: 72.757 | benign  |
0.917 |
TOLERATED | 0.07 |