Search for Variation information by Variation ID:
Detailed information for vg0208665681:
| Variant ID: vg0208665681 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 8665681 |
| Reference Allele: G | Alternative Allele: A |
| Primary Allele: G | Secondary Allele: A |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 313. )
Flanking Sequence (100 bp) in Reference Genome:
TGGCCTGCACTTAGCAACCTATCCGGACAGTCCAACAAGGGGTACAAGGCTTGCACTCACTGTATGGATGAAACAGAAAGTACGTATCTTAAGCACTGTA[G/A]
GAAGGTTGTATACATGGGTCATCGTCGATTCCTTGCAGCAAACCACCCGGTACGGAAGAAAGGCAAGCACTTCGAACATAAGGCCGACCACCGTACGAAT
Reverse complement sequence
ATTCGTACGGTGGTCGGCCTTATGTTCGAAGTGCTTGCCTTTCTTCCGTACCGGGTGGTTTGCTGCAAGGAATCGACGATGACCCATGTATACAACCTTC[C/T]
TACAGTGCTTAAGATACGTACTTTCTGTTTCATCCATACAGTGAGTGCAAGCCTTGTACCCCTTGTTGGACTGTCCGGATAGGTTGCTAAGTGCAGGCCA
Allele Frequencies:
| Populations | Population Size | Frequency of G(primary allele) | Frequency of A(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 19.80% | 0.10% | 2.48% | 77.61% | NA |
| All Indica | 2759 | 5.30% | 0.00% | 1.63% | 93.04% | NA |
| All Japonica | 1512 | 50.30% | 0.40% | 4.63% | 44.64% | NA |
| Aus | 269 | 1.50% | 0.00% | 0.37% | 98.14% | NA |
| Indica I | 595 | 9.40% | 0.00% | 1.51% | 89.08% | NA |
| Indica II | 465 | 3.40% | 0.00% | 0.43% | 96.13% | NA |
| Indica III | 913 | 1.00% | 0.00% | 0.22% | 98.80% | NA |
| Indica Intermediate | 786 | 8.40% | 0.00% | 4.07% | 87.53% | NA |
| Temperate Japonica | 767 | 73.50% | 0.80% | 6.13% | 19.56% | NA |
| Tropical Japonica | 504 | 24.00% | 0.00% | 3.97% | 72.02% | NA |
| Japonica Intermediate | 241 | 31.50% | 0.00% | 1.24% | 67.22% | NA |
| VI/Aromatic | 96 | 1.00% | 0.00% | 0.00% | 98.96% | NA |
| Intermediate | 90 | 24.40% | 0.00% | 1.11% | 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 |
|---|---|---|---|---|---|---|---|---|---|
| vg0208665681 | G -> A | LOC_Os02g15470.1 | missense_variant ; p.Arg333Lys; MODERATE | nonsynonymous_codon ; R333K | Average:11.112; most accessible tissue: Zhenshan97 panicle, score: 16.188 | benign  |
1.207 |
DELETERIOUS | 0.01 |
| vg0208665681 | G -> DEL | LOC_Os02g15470.1 | N | frameshift_variant | Average:11.112; most accessible tissue: Zhenshan97 panicle, score: 16.188 | N | N | N | N |