Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1117664827:

Variant ID: vg1117664827 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17664827
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAATACATTTTTATAACAATATTAACAAGTTTTACCAATAAATACTTCTTTATTTATTATTAACATAACATAGAAAAATCGTTTGGCCGTACTTTTTG[C/T]
ATCTGGGTCCTTTGCCGCCCTCTACTGGAGCGGCAAGTGGCCCAAATACAAAAAGTACGAGCGCAACCTCTTTATGGGCGGCAAAAATTGCAATTAGCCC

Reverse complement sequence

GGGCTAATTGCAATTTTTGCCGCCCATAAAGAGGTTGCGCTCGTACTTTTTGTATTTGGGCCACTTGCCGCTCCAGTAGAGGGCGGCAAAGGACCCAGAT[G/A]
CAAAAAGTACGGCCAAACGATTTTTCTATGTTATGTTAATAATAAATAAAGAAGTATTTATTGGTAAAACTTGTTAATATTGTTATAAAAATGTATTGAA

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	69.60%	29.80%	0.59%	0.00%	NA
All Indica	2759	63.40%	36.50%	0.18%	0.00%	NA
All Japonica	1512	89.60%	10.10%	0.26%	0.00%	NA
Aus	269	10.80%	82.20%	7.06%	0.00%	NA
Indica I	595	51.60%	48.20%	0.17%	0.00%	NA
Indica II	465	48.20%	51.80%	0.00%	0.00%	NA
Indica III	913	79.30%	20.70%	0.00%	0.00%	NA
Indica Intermediate	786	62.70%	36.80%	0.51%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	72.20%	27.20%	0.60%	0.00%	NA
Japonica Intermediate	241	94.60%	5.00%	0.41%	0.00%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	0.00%	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
vg1117664827	C -> T	LOC_Os11g30390.1	missense_variant ; p.Ala996Val; MODERATE	nonsynonymous_codon ; A996V	Average:46.422; most accessible tissue: Zhenshan97 panicle, score: 79.071	unknown	unknown	DELETERIOUS	0.01

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117664827	NA	4.24E-08	mr1073	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
vg1117664827	3.25E-06	3.25E-06	mr1214	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
vg1117664827	NA	9.59E-07	mr1215	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
vg1117664827	NA	3.72E-07	mr1278	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
vg1117664827	NA	2.96E-07	mr1382	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
vg1117664827	NA	4.53E-06	mr1407	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
vg1117664827	NA	5.16E-06	mr1424	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
vg1117664827	NA	3.64E-06	mr1445	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
vg1117664827	NA	1.49E-06	mr1461	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
vg1117664827	NA	2.03E-06	mr1516	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
vg1117664827	NA	6.50E-06	mr1569	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
vg1117664827	NA	1.64E-06	mr1800	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
vg1117664827	NA	3.54E-08	mr1979	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