Search for Variation information by Variation ID:
Detailed information for vg0203136771:
| Variant ID: vg0203136771 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 3136771 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, A: 0.03, others allele: 0.00, population size: 213. )
Flanking Sequence (100 bp) in Reference Genome:
GAACCTGTGAGATGGAGGTTAGACAATTCTAACACTTGCAGATTTGTCAGGTTGAAAAGTTTCGGTGGAATATGCCCTGAAGAGCTGTTGAAGCTCAAGA[A/T]
GAGCACTGTGAGTGATTTCAGCTGGCCGACCTCTGAAGGAATTGCACCAGTAAGCTTATTGTTTCCAAGATTTAGCATTGCAGGGAGAGCATTGGTCATA
Reverse complement sequence
TATGACCAATGCTCTCCCTGCAATGCTAAATCTTGGAAACAATAAGCTTACTGGTGCAATTCCTTCAGAGGTCGGCCAGCTGAAATCACTCACAGTGCTC[T/A]
TCTTGAGCTTCAACAGCTCTTCAGGGCATATTCCACCGAAACTTTTCAACCTGACAAATCTGCAAGTGTTAGAATTGTCTAACCTCCATCTCACAGGTTC
Allele Frequencies:
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 51.20% | 46.50% | 0.02% | 2.29% | NA |
| All Indica | 2759 | 34.80% | 62.70% | 0.00% | 2.50% | NA |
| All Japonica | 1512 | 85.80% | 13.90% | 0.07% | 0.20% | NA |
| Aus | 269 | 17.10% | 82.50% | 0.00% | 0.37% | NA |
| Indica I | 595 | 53.30% | 46.70% | 0.00% | 0.00% | NA |
| Indica II | 465 | 51.80% | 48.00% | 0.00% | 0.22% | NA |
| Indica III | 913 | 12.30% | 83.60% | 0.00% | 4.16% | NA |
| Indica Intermediate | 786 | 36.90% | 59.30% | 0.00% | 3.82% | NA |
| Temperate Japonica | 767 | 75.60% | 24.30% | 0.13% | 0.00% | NA |
| Tropical Japonica | 504 | 98.60% | 1.40% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 91.70% | 7.10% | 0.00% | 1.24% | NA |
| VI/Aromatic | 96 | 63.50% | 5.20% | 0.00% | 31.25% | NA |
| Intermediate | 90 | 61.10% | 33.30% | 0.00% | 5.56% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0203136771 | A -> T | LOC_Os02g06280.1 | missense_variant ; p.Phe192Ile; MODERATE | nonsynonymous_codon ; F192I | Average:55.479; most accessible tissue: Callus, score: 83.936 | benign  |
-1.171 |
TOLERATED | 0.05 |
| vg0203136771 | A -> DEL | LOC_Os02g06280.1 | N | frameshift_variant | Average:55.479; most accessible tissue: Callus, score: 83.936 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0203136771 | NA | 1.72E-06 | mr1527 | 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 |
| vg0203136771 | NA | 1.71E-11 | mr1582_2 | 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 |
| vg0203136771 | NA | 3.22E-07 | mr1582_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 |