Search for Variation information by Variation ID:
Detailed information for vg0512045441:
| Variant ID: vg0512045441 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 12045441 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )
Flanking Sequence (100 bp) in Reference Genome:
AGACGAATCCTGGCCTTCTGCGGCGGTGCTTCTCCCTTCAATGCGGCTAATTCCTTCTCCAAACGATCCACCTTGTCTTCTAGCTTGCAAATCTTACCAC[G/A]
ATTCCGGTCTTCACGATCTTGAGCGGCTAACACAGTCTCCGCACGACTTTCATCCATAGCCCACAACATCTCAACCAAATGCTTCGTGGTAGCATCATTC
Reverse complement sequence
GAATGATGCTACCACGAAGCATTTGGTTGAGATGTTGTGGGCTATGGATGAAAGTCGTGCGGAGACTGTGTTAGCCGCTCAAGATCGTGAAGACCGGAAT[C/T]
GTGGTAAGATTTGCAAGCTAGAAGACAAGGTGGATCGTTTGGAGAAGGAATTAGCCGCATTGAAGGGAGAAGCACCGCCGCAGAAGGCCAGGATTCGTCT
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 | 84.00% | 0.00% | 4.32% | 11.66% | NA |
| All Indica | 2759 | 88.90% | 0.10% | 5.47% | 5.55% | NA |
| All Japonica | 1512 | 84.70% | 0.00% | 3.11% | 12.17% | NA |
| Aus | 269 | 23.00% | 0.00% | 0.74% | 76.21% | NA |
| Indica I | 595 | 92.40% | 0.00% | 7.39% | 0.17% | NA |
| Indica II | 465 | 97.60% | 0.00% | 0.65% | 1.72% | NA |
| Indica III | 913 | 82.40% | 0.00% | 7.67% | 9.97% | NA |
| Indica Intermediate | 786 | 88.70% | 0.30% | 4.33% | 6.74% | NA |
| Temperate Japonica | 767 | 72.40% | 0.00% | 5.61% | 22.03% | NA |
| Tropical Japonica | 504 | 99.20% | 0.00% | 0.00% | 0.79% | NA |
| Japonica Intermediate | 241 | 93.80% | 0.00% | 1.66% | 4.56% | NA |
| VI/Aromatic | 96 | 95.80% | 0.00% | 3.12% | 1.04% | NA |
| Intermediate | 90 | 90.00% | 0.00% | 1.11% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0512045441 | G -> DEL | LOC_Os05g20520.1 | N | frameshift_variant | Average:15.236; most accessible tissue: Zhenshan97 flower, score: 25.98 | N | N | N | N |
| vg0512045441 | G -> A | LOC_Os05g20520.1 | missense_variant ; p.Arg181Cys; MODERATE | nonsynonymous_codon ; R181C | Average:15.236; most accessible tissue: Zhenshan97 flower, score: 25.98 | probably damaging  |
3.16 |
DELETERIOUS | 0.01 |