Search for Variation information by Variation ID:
Detailed information for vg1105161038:
| Variant ID: vg1105161038 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161038 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
CCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTCCCGCCTAGGACTTTGGCGTGGAGGGGGCGGTGGAGTA[C/T]
GAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTGTTCAGCCATTGGGCTGAACAGGAAAAG
Reverse complement sequence
CTTTTCCTGTTCAGCCCAATGGCTGAACAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTC[G/A]
TACTCCACCGCCCCCTCCACGCCAAAGTCCTAGGCGGGAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 83.00% | 0.40% | 2.18% | 14.43% | NA |
| All Indica | 2759 | 76.40% | 0.60% | 3.19% | 19.79% | NA |
| All Japonica | 1512 | 92.60% | 0.10% | 0.60% | 6.75% | NA |
| Aus | 269 | 92.90% | 0.70% | 1.49% | 4.83% | NA |
| Indica I | 595 | 63.90% | 0.00% | 9.41% | 26.72% | NA |
| Indica II | 465 | 70.10% | 0.60% | 1.08% | 28.17% | NA |
| Indica III | 913 | 87.10% | 0.90% | 0.88% | 11.17% | NA |
| Indica Intermediate | 786 | 77.40% | 0.60% | 2.42% | 19.59% | NA |
| Temperate Japonica | 767 | 91.50% | 0.00% | 0.39% | 8.08% | NA |
| Tropical Japonica | 504 | 96.40% | 0.20% | 0.00% | 3.37% | NA |
| Japonica Intermediate | 241 | 88.00% | 0.00% | 2.49% | 9.54% | NA |
| VI/Aromatic | 96 | 92.70% | 0.00% | 0.00% | 7.29% | NA |
| Intermediate | 90 | 82.20% | 0.00% | 2.22% | 15.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161038 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Arg28His; MODERATE | nonsynonymous_codon ; R28H | Average:5.942; most accessible tissue: Callus, score: 11.873 | probably damaging  |
2.33 |
DELETERIOUS | 0.00 |
| vg1105161038 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:5.942; most accessible tissue: Callus, score: 11.873 | N | N | N | N |