Search for Variation information by Variation ID:
Detailed information for vg0222702890:
| Variant ID: vg0222702890 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 22702890 |
| Reference Allele: C | Alternative Allele: T |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 119. )
Flanking Sequence (100 bp) in Reference Genome:
TTAGAGATTCAATTCAATATAATTTTGGATCATGCATGTACTCACTGGAAAGTAAAACCTCCGTCCAAGTTTTTCTTTCCAAGTCCCGCGGACCAATTGA[C/T]
GGAACCGATCCCAAGCCCTACATATGCAGTTGCAAGCTATGATTAATTAATTATTACCTGAGATCAACATAATAGCAATAGATTCCCCGCGACTTTGGAA
Reverse complement sequence
TTCCAAAGTCGCGGGGAATCTATTGCTATTATGTTGATCTCAGGTAATAATTAATTAATCATAGCTTGCAACTGCATATGTAGGGCTTGGGATCGGTTCC[G/A]
TCAATTGGTCCGCGGGACTTGGAAAGAAAAACTTGGACGGAGGTTTTACTTTCCAGTGAGTACATGCATGATCCAAAATTATATTGAATTGAATCTCTAA
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 | 58.70% | 39.00% | 2.31% | 0.00% | NA |
| All Indica | 2759 | 36.20% | 59.90% | 3.88% | 0.00% | NA |
| All Japonica | 1512 | 98.10% | 1.90% | 0.00% | 0.00% | NA |
| Aus | 269 | 50.90% | 49.10% | 0.00% | 0.00% | NA |
| Indica I | 595 | 22.90% | 73.60% | 3.53% | 0.00% | NA |
| Indica II | 465 | 39.80% | 59.60% | 0.65% | 0.00% | NA |
| Indica III | 913 | 38.80% | 53.90% | 7.34% | 0.00% | NA |
| Indica Intermediate | 786 | 41.20% | 56.70% | 2.04% | 0.00% | NA |
| Temperate Japonica | 767 | 99.50% | 0.50% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 95.80% | 4.20% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 98.80% | 1.20% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 76.70% | 22.20% | 1.11% | 0.00% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0222702890 | C -> T | LOC_Os02g37620.1 | missense_variant ; p.Arg671His; MODERATE | nonsynonymous_codon ; R671H | Average:12.857; most accessible tissue: Zhenshan97 flower, score: 19.041 | benign  |
0.857 |
DELETERIOUS | 0.04 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0222702890 | NA | 1.17E-06 | mr1156_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0222702890 | 7.68E-07 | NA | mr1918_2 | 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 |
| vg0222702890 | NA | 1.04E-06 | mr1918_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |