Search for Variation information by Variation ID:
Detailed information for vg1105160088:
| Variant ID: vg1105160088 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5160088 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: A | Secondary Allele: G |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.71, G: 0.29, others allele: 0.00, population size: 31. )
Flanking Sequence (100 bp) in Reference Genome:
AGCTCTTTGGAGGCGATCTTTTCGATCATGCGGTTGTGCCGCACACCCCCCCTGAACGCGTAGATCACCGCGTGTGCAGGGATGCATGGTATGGTGTTGC[A/G]
GACTTGACAGAACCGCTGAATGTATGAGCGAAGTGACTCATCATCCCTTCGCTGGACTGCATGTAAGTCCGCTTCTTCACCTGGGCGCGGATATGTGCCT
Reverse complement sequence
AGGCACATATCCGCGCCCAGGTGAAGAAGCGGACTTACATGCAGTCCAGCGAAGGGATGATGAGTCACTTCGCTCATACATTCAGCGGTTCTGTCAAGTC[T/C]
GCAACACCATACCATGCATCCCTGCACACGCGGTGATCTACGCGTTCAGGGGGGGTGTGCGGCACAACCGCATGATCGAAAAGATCGCCTCCAAAGAGCT
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 10.70% | 1.60% | 16.67% | 71.07% | NA |
| All Indica | 2759 | 1.10% | 2.40% | 9.93% | 86.59% | NA |
| All Japonica | 1512 | 29.80% | 0.50% | 29.76% | 39.88% | NA |
| Aus | 269 | 1.50% | 0.00% | 7.81% | 90.71% | NA |
| Indica I | 595 | 2.50% | 0.80% | 3.53% | 93.11% | NA |
| Indica II | 465 | 1.10% | 0.20% | 4.52% | 94.19% | NA |
| Indica III | 913 | 0.10% | 1.60% | 15.01% | 83.24% | NA |
| Indica Intermediate | 786 | 1.30% | 5.60% | 12.09% | 81.04% | NA |
| Temperate Japonica | 767 | 34.90% | 0.50% | 17.47% | 47.07% | NA |
| Tropical Japonica | 504 | 14.50% | 0.60% | 52.38% | 32.54% | NA |
| Japonica Intermediate | 241 | 45.60% | 0.40% | 21.58% | 32.37% | NA |
| VI/Aromatic | 96 | 5.20% | 0.00% | 26.04% | 68.75% | NA |
| Intermediate | 90 | 15.60% | 1.10% | 20.00% | 63.33% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105160088 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 | N | N | N | N |
| vg1105160088 | A -> G | LOC_Os11g09660.1 | missense_variant ; p.Cys345Arg; MODERATE | nonsynonymous_codon ; C345R | Average:5.954; most accessible tissue: Zhenshan97 flower, score: 11.396 | benign  |
-0.716 |
TOLERATED | 1.00 |