Search for Variation information by Variation ID:

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

Detailed information for vg0825539010:

Variant ID: vg0825539010 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25539010
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: 0.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCCGAGTAGGACTCTTTCCATCTGTGAACTCCATGACGGATTCCCTTAATGTATGCAGAGAGCGTCCGTATACGCGCAGGTATACCATACCGATACG[C/T]
GGCATGTATCGAAGGGTAAAGGGTATACCTTACCCGTAACCCTGACAGTAGCCCCCGATTTCTGCTTAAATGGACTCGTGTAACCGATCGCGACTTCTGG

Reverse complement sequence

CCAGAAGTCGCGATCGGTTACACGAGTCCATTTAAGCAGAAATCGGGGGCTACTGTCAGGGTTACGGGTAAGGTATACCCTTTACCCTTCGATACATGCC[G/A]
CGTATCGGTATGGTATACCTGCGCGTATACGGACGCTCTCTGCATACATTAAGGGAATCCGTCATGGAGTTCACAGATGGAAAGAGTCCTACTCGGACAA

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	83.10%	9.20%	1.97%	5.76%	NA
All Indica	2759	81.90%	5.50%	3.37%	9.21%	NA
All Japonica	1512	99.20%	0.20%	0.00%	0.60%	NA
Aus	269	4.50%	95.50%	0.00%	0.00%	NA
Indica I	595	81.30%	0.70%	4.20%	13.78%	NA
Indica II	465	69.50%	6.90%	1.29%	22.37%	NA
Indica III	913	89.60%	8.20%	2.19%	0.00%	NA
Indica Intermediate	786	80.70%	5.30%	5.34%	8.65%	NA
Temperate Japonica	767	99.00%	0.30%	0.00%	0.78%	NA
Tropical Japonica	504	99.60%	0.20%	0.00%	0.20%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	84.40%	15.60%	0.00%	0.00%	NA
Intermediate	90	82.20%	7.80%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0825539010	C -> T	LOC_Os08g40330.1	upstream_gene_variant ; 3164.0bp to feature; MODIFIER	silent_mutation	Average:33.699; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg0825539010	C -> T	LOC_Os08g40340.1	upstream_gene_variant ; 438.0bp to feature; MODIFIER	silent_mutation	Average:33.699; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg0825539010	C -> T	LOC_Os08g40330-LOC_Os08g40340	intergenic_region ; MODIFIER	silent_mutation	Average:33.699; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N
vg0825539010	C -> DEL	N	N	silent_mutation	Average:33.699; most accessible tissue: Zhenshan97 flag leaf, score: 57.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825539010	NA	2.82E-23	mr1817	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
vg0825539010	NA	1.20E-08	mr1522_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
vg0825539010	NA	1.90E-15	mr1583_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
vg0825539010	NA	5.94E-06	mr1740_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
vg0825539010	7.63E-06	4.02E-22	mr1817_2	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