Search for Variation information by Variation ID:

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

Detailed information for vg0827752431:

Variant ID: vg0827752431 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 27752431
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TTTAAGGAACCATGGGTTGTGGAGTGTAGTTTCTATTATGATGTCTTATTGACATGACACCATAGACACTACTTATGGACACTATGGGTTGGGACTGCCC[T/C]
TATATTTTAGAATGGAGGGAGTAGTAACTAAACTCAAGAATCAACTTTAGTTTGCATATACTCTACTAGGGAACCGGTTTTCTGTAACAGGTCAAGTAGT

Reverse complement sequence

ACTACTTGACCTGTTACAGAAAACCGGTTCCCTAGTAGAGTATATGCAAACTAAAGTTGATTCTTGAGTTTAGTTACTACTCCCTCCATTCTAAAATATA[A/G]
GGGCAGTCCCAACCCATAGTGTCCATAAGTAGTGTCTATGGTGTCATGTCAATAAGACATCATAATAGAAACTACACTCCACAACCCATGGTTCCTTAAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.40%	25.20%	0.13%	0.21%	NA
All Indica	2759	60.60%	38.90%	0.18%	0.36%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	63.20%	36.40%	0.37%	0.00%	NA
Indica I	595	23.40%	76.50%	0.00%	0.17%	NA
Indica II	465	74.00%	25.20%	0.00%	0.86%	NA
Indica III	913	69.70%	29.60%	0.44%	0.33%	NA
Indica Intermediate	786	70.40%	29.30%	0.13%	0.25%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0827752431	T -> C	LOC_Os08g44070.1	upstream_gene_variant ; 3875.0bp to feature; MODIFIER	silent_mutation	Average:42.74; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0827752431	T -> C	LOC_Os08g44060-LOC_Os08g44070	intergenic_region ; MODIFIER	silent_mutation	Average:42.74; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N
vg0827752431	T -> DEL	N	N	silent_mutation	Average:42.74; most accessible tissue: Zhenshan97 panicle, score: 78.302	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0827752431	NA	1.82E-07	mr1739	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
vg0827752431	NA	3.44E-07	mr1739	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
vg0827752431	NA	8.30E-10	mr1265_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
vg0827752431	NA	1.27E-09	mr1265_2	Ind_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
vg0827752431	NA	1.95E-08	mr1528_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
vg0827752431	NA	5.25E-08	mr1528_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