Search for Variation information by Variation ID:
Detailed information for vg1105159860:
| Variant ID: vg1105159860 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5159860 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGCCTCCCCTTTCGGGTGGCCAGCGAAACGCCTTCGACGGCGAGGACATGACCCTCGTCGTCGGAATGGGCTGACCTCTTCTTCCTCCTCCTGTCACGCC[G/A]
CCCTGTCCGAGCAGCAGATCCGGGGACGGCCGAAGCTGCCACACCGGAACCGGAGGGGTTCCAGGTCCATGCCTCTTCCTTACGAGCCACTCGGTCCGCG
Reverse complement sequence
CGCGGACCGAGTGGCTCGTAAGGAAGAGGCATGGACCTGGAACCCCTCCGGTTCCGGTGTGGCAGCTTCGGCCGTCCCCGGATCTGCTGCTCGGACAGGG[C/T]
GGCGTGACAGGAGGAGGAAGAAGAGGTCAGCCCATTCCGACGACGAGGGTCATGTCCTCGCCGTCGAAGGCGTTTCGCTGGCCACCCGAAAGGGGAGGCC
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 | 55.00% | 0.20% | 11.47% | 33.31% | NA |
| All Indica | 2759 | 42.30% | 0.10% | 14.39% | 43.17% | NA |
| All Japonica | 1512 | 86.00% | 0.00% | 2.84% | 11.18% | NA |
| Aus | 269 | 13.00% | 2.20% | 29.74% | 55.02% | NA |
| Indica I | 595 | 23.70% | 0.00% | 7.06% | 69.24% | NA |
| Indica II | 465 | 35.50% | 0.00% | 11.18% | 53.33% | NA |
| Indica III | 913 | 57.60% | 0.20% | 22.34% | 19.82% | NA |
| Indica Intermediate | 786 | 42.70% | 0.10% | 12.60% | 44.53% | NA |
| Temperate Japonica | 767 | 90.60% | 0.00% | 0.13% | 9.26% | NA |
| Tropical Japonica | 504 | 81.30% | 0.00% | 6.15% | 12.50% | NA |
| Japonica Intermediate | 241 | 80.90% | 0.00% | 4.56% | 14.52% | NA |
| VI/Aromatic | 96 | 51.00% | 1.00% | 15.62% | 32.29% | NA |
| Intermediate | 90 | 53.30% | 0.00% | 7.78% | 38.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105159860 | G -> A | LOC_Os11g09660.1 | missense_variant ; p.Arg421Trp; MODERATE | nonsynonymous_codon ; R421W | Average:5.462; most accessible tissue: Zhenshan97 flower, score: 9.663 | probably damaging  |
3.422 |
DELETERIOUS | 0.02 |
| vg1105159860 | G -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.462; most accessible tissue: Zhenshan97 flower, score: 9.663 | N | N | N | N |