Search for Variation information by Variation ID:
Detailed information for vg1126903440:
| Variant ID: vg1126903440 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 26903440 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
GGACGACGAGTGATGTCCATGTGGCTGATAACGGGGAAGAGGAGGAGGTAGGAGTCGATCCTGCTCTGAACATCCCTGAACTTTTCAGCCTGCCTCCCGG[C/T]
CATCACCAACCTGTACATGGCGCTATTGTCCTGGCATGCCATCACAAGCTCGTGCGCCTCCCGGAGCGTGTCGTCGAGCCCGGTGAAGACGCGGCGGGCG
Reverse complement sequence
CGCCCGCCGCGTCTTCACCGGGCTCGACGACACGCTCCGGGAGGCGCACGAGCTTGTGATGGCATGCCAGGACAATAGCGCCATGTACAGGTTGGTGATG[G/A]
CCGGGAGGCAGGCTGAAAAGTTCAGGGATGTTCAGAGCAGGATCGACTCCTACCTCCTCCTCTTCCCCGTTATCAGCCACATGGACATCACTCGTCGTCC
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 | 20.70% | 1.00% | 3.36% | 74.95% | NA |
| All Indica | 2759 | 12.50% | 0.90% | 4.60% | 81.99% | NA |
| All Japonica | 1512 | 39.10% | 0.10% | 1.06% | 59.79% | NA |
| Aus | 269 | 6.70% | 7.80% | 2.60% | 82.90% | NA |
| Indica I | 595 | 20.50% | 0.00% | 7.56% | 71.93% | NA |
| Indica II | 465 | 7.50% | 0.60% | 3.23% | 88.60% | NA |
| Indica III | 913 | 5.60% | 0.80% | 4.27% | 89.38% | NA |
| Indica Intermediate | 786 | 17.40% | 1.90% | 3.56% | 77.10% | NA |
| Temperate Japonica | 767 | 65.20% | 0.10% | 0.91% | 33.77% | NA |
| Tropical Japonica | 504 | 6.30% | 0.00% | 1.19% | 92.46% | NA |
| Japonica Intermediate | 241 | 24.50% | 0.00% | 1.24% | 74.27% | NA |
| VI/Aromatic | 96 | 7.30% | 0.00% | 6.25% | 86.46% | NA |
| Intermediate | 90 | 16.70% | 2.20% | 3.33% | 77.78% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1126903440 | C -> T | LOC_Os11g44460.1 | missense_variant ; p.Ala79Thr; MODERATE | nonsynonymous_codon ; A79T | Average:15.645; most accessible tissue: Callus, score: 62.316 | benign  |
0.729 |
DELETERIOUS | 0.01 |
| vg1126903440 | C -> DEL | LOC_Os11g44460.1 | N | frameshift_variant | Average:15.645; most accessible tissue: Callus, score: 62.316 | N | N | N | N |