Search for Variation information by Variation ID:

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

Detailed information for vg1003520346:

Variant ID: vg1003520346 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 3520346
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

AAATCCTGGAGAGATTAACGAAATCACCATAGGCGCCTCGCTGTCGACGGGTATGTCGCCTACCACTGAAAGCACAACACCGTTAAATCTTAGAAAATTC[G/A]
CTCCCATGGGAAGTCGAACCCAGCACCTCATATCTAAATTCTTCTTGGAATAAAACCCATCAATGAACAATTTTTCTTTAGCACTAACATCACCGGACTG

Reverse complement sequence

CAGTCCGGTGATGTTAGTGCTAAAGAAAAATTGTTCATTGATGGGTTTTATTCCAAGAAGAATTTAGATATGAGGTGCTGGGTTCGACTTCCCATGGGAG[C/T]
GAATTTTCTAAGATTTAACGGTGTTGTGCTTTCAGTGGTAGGCGACATACCCGTCGACAGCGAGGCGCCTATGGTGATTTCGTTAATCTCTCCAGGATTT

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	56.00%	43.80%	0.17%	0.00%	NA
All Indica	2759	49.70%	50.00%	0.25%	0.00%	NA
All Japonica	1512	63.70%	36.20%	0.07%	0.00%	NA
Aus	269	87.70%	12.30%	0.00%	0.00%	NA
Indica I	595	47.70%	52.30%	0.00%	0.00%	NA
Indica II	465	56.30%	43.40%	0.22%	0.00%	NA
Indica III	913	53.00%	46.50%	0.44%	0.00%	NA
Indica Intermediate	786	43.50%	56.20%	0.25%	0.00%	NA
Temperate Japonica	767	91.80%	8.20%	0.00%	0.00%	NA
Tropical Japonica	504	27.40%	72.40%	0.20%	0.00%	NA
Japonica Intermediate	241	50.20%	49.80%	0.00%	0.00%	NA
VI/Aromatic	96	26.00%	74.00%	0.00%	0.00%	NA
Intermediate	90	56.70%	43.30%	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
vg1003520346	G -> A	LOC_Os10g06760.1	downstream_gene_variant ; 1698.0bp to feature; MODIFIER	silent_mutation	Average:71.434; most accessible tissue: Zhenshan97 flower, score: 80.904	N	N	N	N
vg1003520346	G -> A	LOC_Os10g06760-LOC_Os10g06770	intergenic_region ; MODIFIER	silent_mutation	Average:71.434; most accessible tissue: Zhenshan97 flower, score: 80.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1003520346	NA	2.30E-06	mr1121	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
vg1003520346	2.47E-08	6.33E-11	mr1538	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
vg1003520346	1.02E-07	3.22E-07	mr1547	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
vg1003520346	1.20E-13	2.71E-17	mr1547	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
vg1003520346	4.56E-16	1.72E-20	mr1709	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
vg1003520346	7.94E-26	9.80E-34	mr1709	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
vg1003520346	NA	8.90E-06	mr1043_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
vg1003520346	2.12E-10	9.28E-15	mr1538_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
vg1003520346	3.00E-08	5.94E-11	mr1547_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
vg1003520346	7.23E-17	1.69E-25	mr1547_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
vg1003520346	2.20E-23	4.93E-25	mr1709_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
vg1003520346	7.35E-37	2.17E-50	mr1709_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