Search for Variation information by Variation ID:
Detailed information for vg1105159886:
| Variant ID: vg1105159886 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159886 |
| Reference Allele: A | Alternative Allele: G |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 74. )
Flanking Sequence (100 bp) in Reference Genome:
AACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCCGCCCTGTCCGAGCAGCAGATCCGGGG[A/G]
CGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTCTTCCTTACGAGCCACTCGGTCCGCGAGCTGAAAAAGCTCCGCGGTAGTCTG
Reverse complement sequence
CAGACTACCGCGGAGCTTTTTCAGCTCGCGGACCGAGTGGCTCGTAAGGAAGAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCG[T/C]
CCCCGGATCTGCTGCTCGGACAGGGCGGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTT
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 | 22.10% | 10.30% | 7.51% | 60.14% | NA |
| All Indica | 2759 | 8.70% | 0.80% | 8.59% | 81.91% | NA |
| All Japonica | 1512 | 51.40% | 29.40% | 3.11% | 16.14% | NA |
| Aus | 269 | 2.20% | 0.70% | 19.33% | 77.70% | NA |
| Indica I | 595 | 2.90% | 2.20% | 4.71% | 90.25% | NA |
| Indica II | 465 | 4.30% | 0.60% | 4.30% | 90.75% | NA |
| Indica III | 913 | 7.60% | 0.10% | 14.24% | 78.09% | NA |
| Indica Intermediate | 786 | 16.90% | 0.80% | 7.51% | 74.81% | NA |
| Temperate Japonica | 767 | 49.70% | 34.60% | 4.56% | 11.21% | NA |
| Tropical Japonica | 504 | 63.50% | 14.10% | 1.79% | 20.63% | NA |
| Japonica Intermediate | 241 | 31.50% | 44.80% | 1.24% | 22.41% | NA |
| VI/Aromatic | 96 | 2.10% | 4.20% | 13.54% | 80.21% | NA |
| Intermediate | 90 | 21.10% | 14.40% | 6.67% | 57.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159886 | A -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |
| vg1105159886 | A -> G | LOC_Os11g09660.1 | missense_variant ; p.Val412Ala; MODERATE | nonsynonymous_codon ; V412A | Average:5.639; most accessible tissue: Zhenshan97 flower, score: 9.663 | benign  |
-0.382 |
TOLERATED | 1.00 |