Search for Variation information by Variation ID:
Detailed information for vg0825997807:
| Variant ID: vg0825997807 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 25997807 |
| Reference Allele: G | Alternative Allele: T,A |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GACCACTACCTTCTTGAAGTTGCTCTCCGCCATGAAGAAGTCGAGGCACTTGCTCTTCAGCTCCGGGCAGCCGTGCATCTCGGCGCAGCCCAGCGTCGTC[G/T,A]
CCACCGTCTCCACTGACACGCTCTCCCACAGCTTCTGGGCGCACATCAGCTTCAGCCCGTCCAGCGCGTACCTGTCCGCCGCCGCGAGCAAACGCTGATG
Reverse complement sequence
CATCAGCGTTTGCTCGCGGCGGCGGACAGGTACGCGCTGGACGGGCTGAAGCTGATGTGCGCCCAGAAGCTGTGGGAGAGCGTGTCAGTGGAGACGGTGG[C/A,T]
GACGACGCTGGGCTGCGCCGAGATGCACGGCTGCCCGGAGCTGAAGAGCAAGTGCCTCGACTTCTTCATGGCGGAGAGCAACTTCAAGAAGGTAGTGGTC
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.40% | 0.60% | 0.00% | 0.00% | A: 0.02% |
| All Indica | 2759 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.30% | 0.70% | 0.00% | 0.00% | NA |
| Aus | 269 | 94.80% | 4.80% | 0.00% | 0.00% | A: 0.37% |
| 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 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.60% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 97.10% | 2.90% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 97.80% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0825997807 | G -> T | LOC_Os08g41150.1 | missense_variant ; p.Ala298Glu; MODERATE | nonsynonymous_codon ; A298E | Average:68.196; most accessible tissue: Zhenshan97 panicle, score: 84.374 | probably damaging  |
2.122 |
DELETERIOUS | 0.00 |
| vg0825997807 | G -> A | LOC_Os08g41150.1 | missense_variant ; p.Ala298Val; MODERATE | nonsynonymous_codon ; A298V | Average:68.196; most accessible tissue: Zhenshan97 panicle, score: 84.374 | benign |
0.876 |
DELETERIOUS | 0.04 |