Search for Variation information by Variation ID:
Detailed information for vg1105161113:
| Variant ID: vg1105161113 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161113 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 94. )
Flanking Sequence (100 bp) in Reference Genome:
TTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGT[T/C]
CAGCCATTGGGCTGAACAGGAAAAGCTTGGCGCACACGAAAGAGTGCGAGAGCTTAGAAGAACACACGCAGAACCCCCTACCTGGCGCGCCAGATGACGG
Reverse complement sequence
CCGTCATCTGGCGCGCCAGGTAGGGGGTTCTGCGTGTGTTCTTCTAAGCTCTCGCACTCTTTCGTGTGCGCCAAGCTTTTCCTGTTCAGCCCAATGGCTG[A/G]
ACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAA
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 34.20% | 30.70% | 18.92% | 16.25% | NA |
| All Indica | 2759 | 10.80% | 42.40% | 25.55% | 21.20% | NA |
| All Japonica | 1512 | 84.20% | 0.70% | 5.95% | 9.13% | NA |
| Aus | 269 | 0.70% | 81.40% | 13.01% | 4.83% | NA |
| Indica I | 595 | 7.70% | 48.40% | 24.20% | 19.66% | NA |
| Indica II | 465 | 5.80% | 41.10% | 21.51% | 31.61% | NA |
| Indica III | 913 | 9.60% | 45.00% | 27.60% | 17.74% | NA |
| Indica Intermediate | 786 | 17.60% | 35.60% | 26.59% | 20.23% | NA |
| Temperate Japonica | 767 | 88.70% | 0.40% | 2.22% | 8.74% | NA |
| Tropical Japonica | 504 | 80.60% | 1.00% | 9.52% | 8.93% | NA |
| Japonica Intermediate | 241 | 77.60% | 1.20% | 10.37% | 10.79% | NA |
| VI/Aromatic | 96 | 10.40% | 29.20% | 42.71% | 17.71% | NA |
| Intermediate | 90 | 34.40% | 23.30% | 25.56% | 16.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161113 | T -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.249; most accessible tissue: Minghui63 root, score: 13.235 | N | N | N | N |
| vg1105161113 | T -> C | LOC_Os11g09660.1 | missense_variant ; p.Glu3Gly; MODERATE | nonsynonymous_codon ; E3G | Average:6.249; most accessible tissue: Minghui63 root, score: 13.235 | benign  |
1.268 |
DELETERIOUS | 0.01 |