Search for Variation information by Variation ID:
Detailed information for vg1105161011:
| Variant ID: vg1105161011 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 5161011 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GAGGAGGCGACGCTCCCCACCTCGCCGCCCTTCCCCATCACCCGTGGATGTCGAAGTCGCGGATCCTTCGACCCTCTCGAGCGCCTCCTCCCGCCTAGGA[C/T]
TTTGGCGTGGAGGGGGCGGTGGAGTACGAGCTCGACGGCGTGGGTTTGGCTCCCCGTCGTCACCGCTAACACTCGGAGAGAGGTTGTGCGCCTTTGCTTG
Reverse complement sequence
CAAGCAAAGGCGCACAACCTCTCTCCGAGTGTTAGCGGTGACGACGGGGAGCCAAACCCACGCCGTCGAGCTCGTACTCCACCGCCCCCTCCACGCCAAA[G/A]
TCCTAGGCGGGAGGAGGCGCTCGAGAGGGTCGAAGGATCCGCGACTTCGACATCCACGGGTGATGGGGAAGGGCGGCGAGGTGGGGAGCGTCGCCTCCTC
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 | 74.90% | 0.60% | 8.63% | 15.89% | NA |
| All Indica | 2759 | 66.80% | 0.00% | 11.20% | 21.96% | NA |
| All Japonica | 1512 | 89.20% | 1.70% | 2.05% | 7.01% | NA |
| Aus | 269 | 74.30% | 0.00% | 18.96% | 6.69% | NA |
| Indica I | 595 | 48.60% | 0.00% | 20.00% | 31.43% | NA |
| Indica II | 465 | 62.60% | 0.00% | 7.10% | 30.32% | NA |
| Indica III | 913 | 79.40% | 0.00% | 8.76% | 11.83% | NA |
| Indica Intermediate | 786 | 68.60% | 0.00% | 9.80% | 21.63% | NA |
| Temperate Japonica | 767 | 90.10% | 0.80% | 0.65% | 8.47% | NA |
| Tropical Japonica | 504 | 95.60% | 0.00% | 0.99% | 3.37% | NA |
| Japonica Intermediate | 241 | 73.00% | 8.30% | 8.71% | 9.96% | NA |
| VI/Aromatic | 96 | 83.30% | 0.00% | 9.38% | 7.29% | NA |
| Intermediate | 90 | 75.60% | 0.00% | 8.89% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg1105161011 | C -> T | LOC_Os11g09660.1 | missense_variant ; p.Ser37Asn; MODERATE | nonsynonymous_codon ; S37N | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.386 |
TOLERATED | 0.13 |
| vg1105161011 | C -> DEL | LOC_Os11g09660.1 | N | frameshift_variant | Average:6.767; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |