Search for Variation information by Variation ID:
Detailed information for vg1117777874:
| Variant ID: vg1117777874 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17777874 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )
Flanking Sequence (100 bp) in Reference Genome:
GTACTGGCGAAGAACAAGGGCACGTGGAGATCATGAGAGATTTGTCCCAGATTCGGAGAAAGAGATGCTGTGGACCACAATGCTCGAGACATTCACCCTT[C/T]
CTGCGGGTACAGAGGACAAAGTGAAAAGGTGGACTCTGAAGAAAATGGCAGAACAGTTTCAGAGCTTCAAGGGAGATCTGTACCAGAAGTATATACTGAA
Reverse complement sequence
TTCAGTATATACTTCTGGTACAGATCTCCCTTGAAGCTCTGAAACTGTTCTGCCATTTTCTTCAGAGTCCACCTTTTCACTTTGTCCTCTGTACCCGCAG[G/A]
AAGGGTGAATGTCTCGAGCATTGTGGTCCACAGCATCTCTTTCTCCGAATCTGGGACAAATCTCTCATGATCTCCACGTGCCCTTGTTCTTCGCCAGTAC
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 | 0.30% | 0.10% | 3.55% | 96.00% | NA |
| All Indica | 2759 | 0.60% | 0.00% | 4.46% | 94.93% | NA |
| All Japonica | 1512 | 0.00% | 0.30% | 1.26% | 98.48% | NA |
| Aus | 269 | 0.00% | 0.00% | 1.12% | 98.88% | NA |
| Indica I | 595 | 0.30% | 0.20% | 1.85% | 97.65% | NA |
| Indica II | 465 | 0.60% | 0.00% | 11.61% | 87.74% | NA |
| Indica III | 913 | 0.70% | 0.00% | 2.96% | 96.39% | NA |
| Indica Intermediate | 786 | 0.60% | 0.00% | 3.94% | 95.42% | NA |
| Temperate Japonica | 767 | 0.00% | 0.40% | 2.09% | 97.52% | NA |
| Tropical Japonica | 504 | 0.00% | 0.20% | 0.40% | 99.40% | NA |
| Japonica Intermediate | 241 | 0.00% | 0.00% | 0.41% | 99.59% | NA |
| VI/Aromatic | 96 | 0.00% | 0.00% | 16.67% | 83.33% | NA |
| Intermediate | 90 | 0.00% | 0.00% | 7.78% | 92.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117777874 | C -> T | LOC_Os11g30552.1 | missense_variant ; p.Pro276Ser; MODERATE | nonsynonymous_codon ; P276S | Average:11.062; most accessible tissue: Minghui63 panicle, score: 16.27 | probably damaging  |
2.006 |
DELETERIOUS | 0.01 |
| vg1117777874 | C -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:11.062; most accessible tissue: Minghui63 panicle, score: 16.27 | N | N | N | N |