Search for Variation information by Variation ID:

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

Detailed information for vg0822916694:

Variant ID: vg0822916694 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 22916694
Reference Allele: C	Alternative Allele: T,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.04, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:

ATTCCTCCCTTAAATCCTGAGGTGGTATTATTATCCTTAACACTTATTATGGGCCTTTGAGATTTAATAGGATAAATTGGGCCTAGCCCAATTATTCTAA[C/T,G]
AATCCCCACCAAATTTCAAGGCTCATAAGAAATGTTCTCAAGGTTGTGCCTGTTTGATATACCAGGGTTTTGGTGGAGACTGTTAAGTTGAACTTCCTCC

Reverse complement sequence

GGAGGAAGTTCAACTTAACAGTCTCCACCAAAACCCTGGTATATCAAACAGGCACAACCTTGAGAACATTTCTTATGAGCCTTGAAATTTGGTGGGGATT[G/A,C]
TTAGAATAATTGGGCTAGGCCCAATTTATCCTATTAAATCTCAAAGGCCCATAATAAGTGTTAAGGATAATAATACCACCTCAGGATTTAAGGGAGGAAT

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	48.60%	35.30%	11.36%	4.34%	G: 0.38%
All Indica	2759	72.10%	4.00%	16.46%	7.14%	G: 0.33%
All Japonica	1512	1.40%	98.40%	0.20%	0.00%	NA
Aus	269	63.20%	7.10%	26.02%	0.37%	G: 3.35%
Indica I	595	60.80%	2.70%	27.23%	9.08%	G: 0.17%
Indica II	465	65.60%	3.40%	16.56%	13.98%	G: 0.43%
Indica III	913	84.00%	3.40%	9.31%	3.07%	G: 0.22%
Indica Intermediate	786	70.70%	5.90%	16.54%	6.36%	G: 0.51%
Temperate Japonica	767	1.60%	98.20%	0.26%	0.00%	NA
Tropical Japonica	504	0.60%	99.20%	0.20%	0.00%	NA
Japonica Intermediate	241	2.50%	97.50%	0.00%	0.00%	NA
VI/Aromatic	96	84.40%	10.40%	5.21%	0.00%	NA
Intermediate	90	41.10%	45.60%	5.56%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0822916694	C -> G	LOC_Os08g36370.1	upstream_gene_variant ; 4723.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> G	LOC_Os08g36350.1	downstream_gene_variant ; 241.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> G	LOC_Os08g36360.1	downstream_gene_variant ; 1016.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> G	LOC_Os08g36350-LOC_Os08g36360	intergenic_region ; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> T	LOC_Os08g36370.1	upstream_gene_variant ; 4723.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> T	LOC_Os08g36350.1	downstream_gene_variant ; 241.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> T	LOC_Os08g36360.1	downstream_gene_variant ; 1016.0bp to feature; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> T	LOC_Os08g36350-LOC_Os08g36360	intergenic_region ; MODIFIER	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N
vg0822916694	C -> DEL	N	N	silent_mutation	Average:27.292; most accessible tissue: Zhenshan97 flower, score: 43.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0822916694	2.53E-06	1.27E-06	mr1946_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
vg0822916694	2.53E-06	1.27E-06	mr1948_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