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Detailed information for vg0914860717:
| Variant ID: vg0914860717 (JBrowse) | Variation Type: SNP |
| Chromosome: chr09 | Position: 14860717 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 277. )
Flanking Sequence (100 bp) in Reference Genome:
TATGCCATGGGGTTTTATCAACTGCCTGAAGGGATTTATCAGAAATTTGACTCTATTAGAGGAAAATATTATTGGGCTAGCAATAAGCAGGGGAGAAAAT[A/T]
CCACATTGTGAGATGGATTGACCTAGCCTTCTCAAAAGAGTTTGGTGGCATTGGTCTAATTGAAACTAGAACTCTTAACACAGCTTTGCTTGCCAAGTGG
Reverse complement sequence
CCACTTGGCAAGCAAAGCTGTGTTAAGAGTTCTAGTTTCAATTAGACCAATGCCACCAAACTCTTTTGAGAAGGCTAGGTCAATCCATCTCACAATGTGG[T/A]
ATTTTCTCCCCTGCTTATTGCTAGCCCAATAATATTTTCCTCTAATAGAGTCAAATTTCTGATAAATCCCTTCAGGCAGTTGATAAAACCCCATGGCATA
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.60% | 0.30% | 0.17% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 98.70% | 0.70% | 0.53% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 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 | 99.90% | 0.00% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 96.60% | 2.00% | 1.39% | 0.00% | NA |
| Japonica Intermediate | 241 | 99.60% | 0.40% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0914860717 | A -> T | LOC_Os09g24880.1 | missense_variant ; p.Tyr32Phe; MODERATE | nonsynonymous_codon ; Y32F | Average:57.572; most accessible tissue: Callus, score: 82.969 | benign  |
0.804 |
TOLERATED | 0.26 |