Search for Variation information by Variation ID:

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

Detailed information for vg1124633481:

Variant ID: vg1124633481 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24633481
Reference Allele: G	Alternative Allele: T,C
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAGTTTTTGGGAACTAAACAGGGCCAAAAACTTTTGGAATCCCATTATGCAGCCTAGCTACTTGGATGTCCAAAAATTTCAAAGTGGCATTACTAGAGAA[G/T,C]
GATCCTCTCTATACAAATCAATATAACCCGTAAATTAATTGTACCTTTATTATGTTCAGGGACATGACAATGAAAACAATAAGTCAAATGTTGATGACCT

Reverse complement sequence

AGGTCATCAACATTTGACTTATTGTTTTCATTGTCATGTCCCTGAACATAATAAAGGTACAATTAATTTACGGGTTATATTGATTTGTATAGAGAGGATC[C/A,G]
TTCTCTAGTAATGCCACTTTGAAATTTTTGGACATCCAAGTAGCTAGGCTGCATAATGGGATTCCAAAAGTTTTTGGCCCTGTTTAGTTCCCAAAAACTT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.40%	38.50%	0.02%	0.00%	NA
All Indica	2759	94.60%	5.40%	0.00%	0.00%	NA
All Japonica	1512	6.30%	93.70%	0.07%	0.00%	NA
Aus	269	40.90%	59.10%	0.00%	0.00%	NA
Indica I	595	99.00%	1.00%	0.00%	0.00%	NA
Indica II	465	97.00%	3.00%	0.00%	0.00%	NA
Indica III	913	92.90%	7.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.90%	8.10%	0.00%	0.00%	NA
Temperate Japonica	767	3.80%	96.20%	0.00%	0.00%	NA
Tropical Japonica	504	7.70%	92.30%	0.00%	0.00%	NA
Japonica Intermediate	241	11.20%	88.40%	0.41%	0.00%	NA
VI/Aromatic	96	45.80%	54.20%	0.00%	0.00%	NA
Intermediate	90	50.00%	50.00%	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
vg1124633481	G -> T	LOC_Os11g41110.1	downstream_gene_variant ; 1837.0bp to feature; MODIFIER	silent_mutation	Average:50.583; most accessible tissue: Callus, score: 84.486	N	N	N	N
vg1124633481	G -> T	LOC_Os11g41110-LOC_Os11g41130	intergenic_region ; MODIFIER	silent_mutation	Average:50.583; most accessible tissue: Callus, score: 84.486	N	N	N	N
vg1124633481	G -> C	LOC_Os11g41110.1	downstream_gene_variant ; 1837.0bp to feature; MODIFIER	N	Average:50.583; most accessible tissue: Callus, score: 84.486	N	N	N	N
vg1124633481	G -> C	LOC_Os11g41110-LOC_Os11g41130	intergenic_region ; MODIFIER	N	Average:50.583; most accessible tissue: Callus, score: 84.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124633481	NA	3.77E-12	mr1034	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
vg1124633481	NA	3.75E-11	mr1316	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
vg1124633481	NA	1.21E-26	mr1537	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
vg1124633481	NA	6.23E-20	mr1541	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
vg1124633481	NA	5.78E-18	mr1566	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
vg1124633481	NA	1.18E-09	mr1578	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
vg1124633481	NA	5.94E-11	mr1609	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
vg1124633481	NA	6.92E-61	mr1671	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
vg1124633481	NA	2.50E-18	mr1700	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
vg1124633481	4.27E-06	NA	mr1758	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
vg1124633481	NA	1.96E-12	mr1819	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
vg1124633481	NA	3.10E-07	mr1836	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
vg1124633481	NA	3.15E-23	mr1841	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
vg1124633481	NA	2.73E-15	mr1916	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
vg1124633481	NA	1.07E-09	mr1945	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
vg1124633481	NA	2.26E-16	mr1836_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