Search for Variation information by Variation ID:

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

Detailed information for vg0415195707:

Variant ID: vg0415195707 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 15195707
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.93, T: 0.07, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

ATCTCAATGGCATTCCTAGCTGCTACCCCAAGTTTTACTGCATATGTTCATAGCTGGCTATTAACATTTTGTGTGGAGCTATGTTAGGATTCCAGATTTC[A/T]
AGGATGGATATACTAGTATGTATGAATATGCCCCTATTGTATGAAATATATTACCGAGGAGCGGAGTTTCAAATTCAGATCAAGTGCAGTGTTTGGAGAG

Reverse complement sequence

CTCTCCAAACACTGCACTTGATCTGAATTTGAAACTCCGCTCCTCGGTAATATATTTCATACAATAGGGGCATATTCATACATACTAGTATATCCATCCT[T/A]
GAAATCTGGAATCCTAACATAGCTCCACACAAAATGTTAATAGCCAGCTATGAACATATGCAGTAAAACTTGGGGTAGCAGCTAGGAATGCCATTGAGAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.70%	14.10%	2.43%	11.79%	NA
All Indica	2759	69.60%	14.10%	3.55%	12.79%	NA
All Japonica	1512	86.10%	0.20%	0.86%	12.83%	NA
Aus	269	2.20%	97.00%	0.74%	0.00%	NA
Indica I	595	84.70%	9.90%	2.18%	3.19%	NA
Indica II	465	64.10%	24.90%	4.95%	6.02%	NA
Indica III	913	60.40%	11.70%	3.07%	24.86%	NA
Indica Intermediate	786	72.10%	13.50%	4.33%	10.05%	NA
Temperate Japonica	767	75.10%	0.10%	1.56%	23.21%	NA
Tropical Japonica	504	99.00%	0.20%	0.00%	0.79%	NA
Japonica Intermediate	241	94.20%	0.40%	0.41%	4.98%	NA
VI/Aromatic	96	89.60%	6.20%	0.00%	4.17%	NA
Intermediate	90	81.10%	10.00%	2.22%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0415195707	A -> DEL	N	N	silent_mutation	Average:44.89; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0415195707	A -> T	LOC_Os04g26100.1	upstream_gene_variant ; 1029.0bp to feature; MODIFIER	silent_mutation	Average:44.89; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N
vg0415195707	A -> T	LOC_Os04g26090-LOC_Os04g26100	intergenic_region ; MODIFIER	silent_mutation	Average:44.89; most accessible tissue: Zhenshan97 panicle, score: 72.468	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0415195707	NA	7.60E-06	mr1123	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
vg0415195707	NA	6.51E-08	mr1496	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
vg0415195707	NA	2.36E-06	mr1815	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
vg0415195707	NA	2.20E-06	mr1936	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
vg0415195707	NA	9.61E-06	mr1158_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
vg0415195707	NA	3.76E-14	mr1846_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