Search for Variation information by Variation ID:
Detailed information for vg0208664610:
| Variant ID: vg0208664610 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8664610 |
| Reference Allele: C | Alternative Allele: G |
| Primary Allele: C | Secondary Allele: G |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TCCCACGGAGAGCAAGGTGTTGAAATGGAAGAAGATGAAGTGGAAGACGACAATATTCCGGACTTTGCTCAGTATGTTGGATTTGAAGGAAATAGCTGCT[C/G]
ATGGTAACGACGTTGCGGATGATCTTGGTCAGATGTTGCAGGACGCCAGGGAAGACTGCGAAAGTGAAAAGGAGGCCCATAAATTGGACAAGATGTTGGA
Reverse complement sequence
TCCAACATCTTGTCCAATTTATGGGCCTCCTTTTCACTTTCGCAGTCTTCCCTGGCGTCCTGCAACATCTGACCAAGATCATCCGCAACGTCGTTACCAT[G/C]
AGCAGCTATTTCCTTCAAATCCAACATACTGAGCAAAGTCCGGAATATTGTCGTCTTCCACTTCATCTTCTTCCATTTCAACACCTTGCTCTCCGTGGGA
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 | 13.00% | 4.00% | 3.43% | 79.58% | NA |
| All Indica | 2759 | 3.50% | 0.10% | 2.50% | 93.84% | NA |
| All Japonica | 1512 | 32.70% | 12.20% | 5.69% | 49.34% | NA |
| Aus | 269 | 1.10% | 0.40% | 0.37% | 98.14% | NA |
| Indica I | 595 | 8.10% | 0.00% | 2.35% | 89.58% | NA |
| Indica II | 465 | 2.20% | 0.00% | 1.94% | 95.91% | NA |
| Indica III | 913 | 0.70% | 0.30% | 1.53% | 97.48% | NA |
| Indica Intermediate | 786 | 4.20% | 0.10% | 4.07% | 91.60% | NA |
| Temperate Japonica | 767 | 55.90% | 19.20% | 1.96% | 22.95% | NA |
| Tropical Japonica | 504 | 3.80% | 2.40% | 13.69% | 80.16% | NA |
| Japonica Intermediate | 241 | 19.50% | 10.80% | 0.83% | 68.88% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 18.90% | 0.00% | 6.67% | 74.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0208664610 | C -> G | LOC_Os02g15470.1 | missense_variant ; p.His23Asp; MODERATE | nonsynonymous_codon ; H23D | Average:4.663; most accessible tissue: Minghui63 panicle, score: 7.125 | benign  |
-1.041 |
TOLERATED | 1.00 |
| vg0208664610 | C -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:4.663; most accessible tissue: Minghui63 panicle, score: 7.125 | N | N | N | N |