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Detailed information for vg0335314719:
| Variant ID: vg0335314719 (JBrowse) | Variation Type: SNP |
| Chromosome: chr03 | Position: 35314719 |
| Reference Allele: T | Alternative Allele: A |
| Primary Allele: T | Secondary Allele: A |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
GGTTGCAATCTCCACCTCTGTAACAAACTCTTGTATTGCATCAACTGAAGGTTTCAGAATCTTTACAGCTGATAATGTGCCATCAAATAGTTGTGCCTTG[T/A]
AAACTTGGCTTGTTCCTCCCTTTCCAATTAACATATCTGCATTGGTGTAAAAGAAAATCAGCAGACAACTTTGCCAAAAAGCCTGTGAATCAAAGTAATG
Reverse complement sequence
CATTACTTTGATTCACAGGCTTTTTGGCAAAGTTGTCTGCTGATTTTCTTTTACACCAATGCAGATATGTTAATTGGAAAGGGAGGAACAAGCCAAGTTT[A/T]
CAAGGCACAACTATTTGATGGCACATTATCAGCTGTAAAGATTCTGAAACCTTCAGTTGATGCAATACAAGAGTTTGTTACAGAGGTGGAGATTGCAACC
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 88.80% | 11.10% | 0.08% | 0.00% | NA |
| All Indica | 2759 | 81.10% | 18.80% | 0.11% | 0.00% | NA |
| All Japonica | 1512 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 61.20% | 38.50% | 0.34% | 0.00% | NA |
| Indica II | 465 | 86.70% | 13.30% | 0.00% | 0.00% | NA |
| Indica III | 913 | 86.20% | 13.80% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 86.90% | 13.00% | 0.13% | 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 | 92.20% | 6.70% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0335314719 | T -> A | LOC_Os03g62340.1 | missense_variant ; p.Tyr608Phe; MODERATE | nonsynonymous_codon ; Y608F | Average:62.603; most accessible tissue: Callus, score: 78.573 | benign  |
0.699 |
TOLERATED | 0.14 |