Search for Variation information by Variation ID:
Detailed information for vg0510478778:
| Variant ID: vg0510478778 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 10478778 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
TCGAATAGATTATACTCTGATCAGAGGTGTACAACTTTACCCACAAGACACATCTTCCTCACGTGCAACCACGTGCCACATACCACCACGGTATACAGAC[G/A]
GAAGACGTGACATAGTTTCCAACCCATCCTAGCCATAGACAAGAGTACCGACCCAATCCCACCTACGGCCGGAACCCCCGGGACAGGTAGGCAGGACTGA
Reverse complement sequence
TCAGTCCTGCCTACCTGTCCCGGGGGTTCCGGCCGTAGGTGGGATTGGGTCGGTACTCTTGTCTATGGCTAGGATGGGTTGGAAACTATGTCACGTCTTC[C/T]
GTCTGTATACCGTGGTGGTATGTGGCACGTGGTTGCACGTGAGGAAGATGTGTCTTGTGGGTAAAGTTGTACACCTCTGATCAGAGTATAATCTATTCGA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 91.10% | 5.60% | 3.26% | 0.00% | NA |
| All Indica | 2759 | 91.60% | 4.50% | 3.88% | 0.00% | NA |
| All Japonica | 1512 | 99.80% | 0.10% | 0.13% | 0.00% | NA |
| Aus | 269 | 34.60% | 51.30% | 14.13% | 0.00% | NA |
| Indica I | 595 | 99.30% | 0.30% | 0.34% | 0.00% | NA |
| Indica II | 465 | 99.40% | 0.20% | 0.43% | 0.00% | NA |
| Indica III | 913 | 81.70% | 10.80% | 7.45% | 0.00% | NA |
| Indica Intermediate | 786 | 92.60% | 2.90% | 4.45% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.40% | 0.20% | 0.40% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 99.00% | 0.00% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 91.10% | 2.20% | 6.67% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0510478778 | G -> A | LOC_Os05g18220.1 | missense_variant ; p.Arg47Cys; MODERATE | nonsynonymous_codon ; R47C | Average:22.596; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | probably damaging  |
2.729 |
TOLERATED | 0.07 |