Search for Variation information by Variation ID:
Detailed information for vg0516130082:
| Variant ID: vg0516130082 (JBrowse) | Variation Type: SNP |
| Chromosome: chr05 | Position: 16130082 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.08, others allele: 0.00, population size: 73. )
Flanking Sequence (100 bp) in Reference Genome:
TAGATACTCTTGAAATTGATCCAGAGAATATCTTCTCCTAGCAAGAAGTCCGTGTCCCTAATCCTCGCTCCAATTATCTCTCTACCGGTGGCGCTCATTT[C/T]
CATGTACAATTGATGAAATTTGTACATCTGTGTCGGTAGGGACTGCAGCTGCTCAGGCTTGACAAGCGATTTACTGAGTTCATGCTTGTATTTCACTTCC
Reverse complement sequence
GGAAGTGAAATACAAGCATGAACTCAGTAAATCGCTTGTCAAGCCTGAGCAGCTGCAGTCCCTACCGACACAGATGTACAAATTTCATCAATTGTACATG[G/A]
AAATGAGCGCCACCGGTAGAGAGATAATTGGAGCGAGGATTAGGGACACGGACTTCTTGCTAGGAGAAGATATTCTCTGGATCAATTTCAAGAGTATCTA
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 | 32.60% | 18.60% | 2.90% | 45.87% | NA |
| All Indica | 2759 | 12.50% | 28.00% | 3.91% | 55.56% | NA |
| All Japonica | 1512 | 75.50% | 0.40% | 0.79% | 23.28% | NA |
| Aus | 269 | 4.10% | 0.00% | 4.09% | 91.82% | NA |
| Indica I | 595 | 4.90% | 30.80% | 5.21% | 59.16% | NA |
| Indica II | 465 | 16.80% | 16.30% | 4.95% | 61.94% | NA |
| Indica III | 913 | 19.20% | 26.90% | 2.74% | 51.15% | NA |
| Indica Intermediate | 786 | 8.10% | 34.00% | 3.69% | 54.20% | NA |
| Temperate Japonica | 767 | 93.00% | 0.00% | 0.13% | 6.91% | NA |
| Tropical Japonica | 504 | 46.80% | 0.40% | 1.98% | 50.79% | NA |
| Japonica Intermediate | 241 | 80.10% | 1.70% | 0.41% | 17.84% | NA |
| VI/Aromatic | 96 | 11.50% | 85.40% | 0.00% | 3.12% | NA |
| Intermediate | 90 | 34.40% | 22.20% | 6.67% | 36.67% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0516130082 | C -> T | LOC_Os05g27690.1 | missense_variant ; p.Glu489Lys; MODERATE | nonsynonymous_codon ; E489K | Average:33.444; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | possibly damaging  |
1.77 |
DELETERIOUS | 0.00 |
| vg0516130082 | C -> DEL | LOC_Os05g27690.1 | N | frameshift_variant | Average:33.444; most accessible tissue: Zhenshan97 flag leaf, score: 43.728 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0516130082 | 5.84E-06 | 1.13E-06 | mr1218_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |