Search for Variation information by Variation ID:
Detailed information for vg1117778384:
| Variant ID: vg1117778384 (JBrowse) | Variation Type: SNP |
| Chromosome: chr11 | Position: 17778384 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 381. )
Flanking Sequence (100 bp) in Reference Genome:
CGGCGATCAGATACGAGAGGCTGCGCGACGACTAACAGATGCAGTGGAAGCCTCCTCTCAGGGCACGTTCCGACCAGACAGAGATAGGGACGAGCTGACA[C/G]
TCGCCCTGCAGACTCCAGAGCATCCAGGACGAACACGAGGGAAAGGGGTGATTCCTTGGAAGATTGGTTTCAAGGAGGACATCCACACGTACAGGAGTCG
Reverse complement sequence
CGACTCCTGTACGTGTGGATGTCCTCCTTGAAACCAATCTTCCAAGGAATCACCCCTTTCCCTCGTGTTCGTCCTGGATGCTCTGGAGTCTGCAGGGCGA[G/C]
TGTCAGCTCGTCCCTATCTCTGTCTGGTCGGAACGTGCCCTGAGAGGAGGCTTCCACTGCATCTGTTAGTCGTCGCGCAGCCTCTCGTATCTGATCGCCG
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of G(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 12.40% | 0.50% | 12.04% | 75.07% | NA |
| All Indica | 2759 | 8.00% | 0.80% | 4.46% | 86.77% | NA |
| All Japonica | 1512 | 21.60% | 0.00% | 24.54% | 53.84% | NA |
| Aus | 269 | 4.50% | 0.00% | 13.01% | 82.53% | NA |
| Indica I | 595 | 3.50% | 1.00% | 3.70% | 91.76% | NA |
| Indica II | 465 | 19.10% | 0.00% | 3.44% | 77.42% | NA |
| Indica III | 913 | 7.20% | 1.20% | 5.59% | 85.98% | NA |
| Indica Intermediate | 786 | 5.60% | 0.60% | 4.33% | 89.44% | NA |
| Temperate Japonica | 767 | 18.40% | 0.00% | 31.03% | 50.59% | NA |
| Tropical Japonica | 504 | 16.30% | 0.00% | 10.32% | 73.41% | NA |
| Japonica Intermediate | 241 | 43.20% | 0.00% | 33.61% | 23.24% | NA |
| VI/Aromatic | 96 | 14.60% | 0.00% | 30.21% | 55.21% | NA |
| Intermediate | 90 | 15.60% | 0.00% | 12.22% | 72.22% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1117778384 | C -> DEL | LOC_Os11g30552.1 | N | frameshift_variant | Average:8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |
| vg1117778384 | C -> G | LOC_Os11g30552.1 | missense_variant ; p.Leu446Val; MODERATE | nonsynonymous_codon ; L446V | Average:8.604; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
0.814 |
DELETERIOUS | 0.00 |