Search for Variation information by Variation ID:

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

Detailed information for vg1125633880:

Variant ID: vg1125633880 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25633880
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.05, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGGCTAGTATCATTACTGTTTCAGCTGATCAGCGCCGTCGAAGAGCTCTGGAGCCTCGCTCTCTGGAGAACTTCTGTTCCGACGAGCTTACCCGCTGG[G/T]
TAAAGTCGGTTGGCACTATGGGACGATCATCATCTTCATCGCCATCATTACCACCCATCGCCATTGTACCACCACCACCCACACCCAGGCCAGCTCAAGG

Reverse complement sequence

CCTTGAGCTGGCCTGGGTGTGGGTGGTGGTGGTACAATGGCGATGGGTGGTAATGATGGCGATGAAGATGATGATCGTCCCATAGTGCCAACCGACTTTA[C/A]
CCAGCGGGTAAGCTCGTCGGAACAGAAGTTCTCCAGAGAGCGAGGCTCCAGAGCTCTTCGACGGCGCTGATCAGCTGAAACAGTAATGATACTAGCCGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.80%	25.50%	1.33%	20.29%	NA
All Indica	2759	28.50%	39.00%	1.81%	30.63%	NA
All Japonica	1512	92.60%	5.70%	0.26%	1.46%	NA
Aus	269	66.50%	1.50%	1.86%	30.11%	NA
Indica I	595	49.10%	35.10%	1.01%	14.79%	NA
Indica II	465	8.00%	78.10%	1.08%	12.90%	NA
Indica III	913	30.80%	25.70%	2.08%	41.40%	NA
Indica Intermediate	786	22.50%	34.40%	2.54%	40.59%	NA
Temperate Japonica	767	95.40%	2.50%	0.39%	1.69%	NA
Tropical Japonica	504	89.90%	9.10%	0.20%	0.79%	NA
Japonica Intermediate	241	89.20%	8.70%	0.00%	2.07%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	55.60%	27.80%	4.44%	12.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125633880	G -> T	LOC_Os11g42590.1	missense_variant ; p.Val201Leu; MODERATE	nonsynonymous_codon ; V201L	Average:38.281; most accessible tissue: Zhenshan97 panicle, score: 82.888	unknown	unknown	TOLERATED	0.36
vg1125633880	G -> DEL	LOC_Os11g42590.1	N	frameshift_variant	Average:38.281; most accessible tissue: Zhenshan97 panicle, score: 82.888	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125633880	NA	2.73E-12	Grain_thickness	Ind_All	YES	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1125633880	NA	1.21E-16	Grain_width	Ind_All	Not	Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1125633880	NA	5.17E-06	mr1130	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
vg1125633880	NA	5.42E-06	mr1268	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
vg1125633880	NA	7.10E-06	mr1398	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
vg1125633880	NA	5.35E-12	mr1720	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
vg1125633880	NA	7.39E-06	mr1720	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
vg1125633880	NA	2.19E-06	mr1942	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