Search for Variation information by Variation ID:
Detailed information for vg0200562288:
| Variant ID: vg0200562288 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 562288 |
| 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: 372. )
Flanking Sequence (100 bp) in Reference Genome:
CCCCTCTTGGATGTTGATGATGCATTCTCTGCCAATATCCTAGACAAAATGTCTGCTTGCTTTGAGTACCCTCCAGCTTTTAAGCTGTCCATCAGGGCAT[C/T]
GCAACCCTTTTGATCCACGACACCTCCTTTGTTCTTGATCTTGCAAAGCATGGAGTATGCAGGCAATGTCTTCTCCTCAGTGTACAGGGCCTCCAAGACT
Reverse complement sequence
AGTCTTGGAGGCCCTGTACACTGAGGAGAAGACATTGCCTGCATACTCCATGCTTTGCAAGATCAAGAACAAAGGAGGTGTCGTGGATCAAAAGGGTTGC[G/A]
ATGCCCTGATGGACAGCTTAAAAGCTGGAGGGTACTCAAAGCAAGCAGACATTTTGTCTAGGATATTGGCAGAGAATGCATCATCAACATCCAAGAGGGG
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 | 99.90% | 0.10% | 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 | 97.40% | 2.20% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0200562288 | C -> T | LOC_Os02g02020.1 | missense_variant ; p.Asp707Asn; MODERATE | nonsynonymous_codon ; D707N | Average:66.284; most accessible tissue: Callus, score: 83.585 | possibly damaging  |
1.653 |
DELETERIOUS | 0.02 |