Search for Variation information by Variation ID:
Detailed information for vg1202830841:
| Variant ID: vg1202830841 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 2830841 |
| Reference Allele: C | Alternative Allele: A |
| Primary Allele: C | Secondary Allele: A |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 345. )
Flanking Sequence (100 bp) in Reference Genome:
TTGTGCAGAATGGTCTCCATGAAGAGGTATTGTGTTTATTTCAGAGTACACAAAGGGAAGGAATGCAATTGACTGAATTCACTGTTTCATCTATCCTCAG[C/A]
ACATGTGCAAGCTTAGCATTGATAATTGAAGGAACACAGGTGCATGCAGTTATTGTTAAGCATGGTTTTCATAGGAACCTCTTTGTAGCAACATCTCTTG
Reverse complement sequence
CAAGAGATGTTGCTACAAAGAGGTTCCTATGAAAACCATGCTTAACAATAACTGCATGCACCTGTGTTCCTTCAATTATCAATGCTAAGCTTGCACATGT[G/T]
CTGAGGATAGATGAAACAGTGAATTCAGTCAATTGCATTCCTTCCCTTTGTGTACTCTGAAATAAACACAATACCTCTTCATGGAGACCATTCTGCACAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 95.70% | 4.30% | 0.02% | 0.00% | NA |
| All Indica | 2759 | 96.60% | 3.40% | 0.04% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 62.10% | 37.90% | 0.00% | 0.00% | NA |
| Indica I | 595 | 93.90% | 6.10% | 0.00% | 0.00% | NA |
| Indica II | 465 | 99.80% | 0.20% | 0.00% | 0.00% | NA |
| Indica III | 913 | 96.60% | 3.40% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 96.60% | 3.30% | 0.13% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 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 | 98.90% | 1.10% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1202830841 | C -> A | LOC_Os12g06070.1 | missense_variant ; p.Ser266Arg; MODERATE | nonsynonymous_codon ; S266R | Average:46.946; most accessible tissue: Zhenshan97 young leaf, score: 67.83 | possibly damaging  |
1.871 |
TOLERATED | 0.46 |