Search for Variation information by Variation ID:

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

Detailed information for vg1125259799:

Variant ID: vg1125259799 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25259799
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGTGGTGTGTTCCTTACATTCTTTTCATTAAGGGTACAGTGTATATTTCTTCAGAAATTTTCTGTAACATGTTCTGATTTGTGGAGCTGAGGTGATTT[G/A]
GCAAGTTCATCCCATTTTATTCTGAGCAATACTGCAAATGTATTGAAGACTGAAGAGCTTGATATAATAGACTAATTGGGTATGAACTGTAGATATTATC

Reverse complement sequence

GATAATATCTACAGTTCATACCCAATTAGTCTATTATATCAAGCTCTTCAGTCTTCAATACATTTGCAGTATTGCTCAGAATAAAATGGGATGAACTTGC[C/T]
AAATCACCTCAGCTCCACAAATCAGAACATGTTACAGAAAATTTCTGAAGAAATATACACTGTACCCTTAATGAAAAGAATGTAAGGAACACACCACCAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	80.10%	19.90%	0.02%	0.00%	NA
All Indica	2759	79.60%	20.40%	0.04%	0.00%	NA
All Japonica	1512	82.50%	17.50%	0.00%	0.00%	NA
Aus	269	66.50%	33.50%	0.00%	0.00%	NA
Indica I	595	48.40%	51.60%	0.00%	0.00%	NA
Indica II	465	78.90%	20.90%	0.22%	0.00%	NA
Indica III	913	92.70%	7.30%	0.00%	0.00%	NA
Indica Intermediate	786	88.30%	11.70%	0.00%	0.00%	NA
Temperate Japonica	767	70.40%	29.60%	0.00%	0.00%	NA
Tropical Japonica	504	98.40%	1.60%	0.00%	0.00%	NA
Japonica Intermediate	241	88.00%	12.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	75.60%	24.40%	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
vg1125259799	G -> A	LOC_Os11g42010.1	downstream_gene_variant ; 3457.0bp to feature; MODIFIER	silent_mutation	Average:46.51; most accessible tissue: Callus, score: 72.92	N	N	N	N
vg1125259799	G -> A	LOC_Os11g42000.1	intron_variant ; MODIFIER	silent_mutation	Average:46.51; most accessible tissue: Callus, score: 72.92	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125259799	6.00E-06	4.16E-09	mr1191	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
vg1125259799	NA	5.01E-06	mr1291	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
vg1125259799	2.44E-06	NA	mr1484	Jap_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
vg1125259799	4.54E-11	1.36E-13	mr1530	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
vg1125259799	7.00E-09	3.32E-11	mr1530	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
vg1125259799	6.47E-07	1.08E-09	mr1530	Jap_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
vg1125259799	3.30E-06	9.81E-11	mr1644	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
vg1125259799	NA	3.52E-07	mr1662	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
vg1125259799	4.90E-08	4.09E-14	mr1662	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
vg1125259799	1.78E-09	NA	mr1745	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
vg1125259799	1.63E-06	2.32E-10	mr1745	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
vg1125259799	8.36E-07	NA	mr1745	Jap_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
vg1125259799	NA	1.67E-07	mr1904	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
vg1125259799	8.44E-09	5.19E-18	mr1191_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
vg1125259799	6.71E-10	NA	mr1530_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
vg1125259799	3.30E-06	2.47E-10	mr1530_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
vg1125259799	2.29E-08	1.06E-13	mr1530_2	Jap_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
vg1125259799	NA	5.81E-07	mr1543_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
vg1125259799	3.69E-08	1.62E-15	mr1662_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
vg1125259799	4.17E-06	NA	mr1745_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
vg1125259799	NA	3.53E-13	mr1745_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