Search for Variation information by Variation ID:

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

Detailed information for vg0412497804:

Variant ID: vg0412497804 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12497804
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.03, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCCAATTGTTATATCTCCTCCATCCGAACTCCGAATTGACCTGTTTATTTTCTTAAGTTAATTCTTCAAAAGTTGAGCTCTATCTTCCGATTTAATT[A/G]
GTTATTTTATTTGTTGTTATTTTTCTGCCTTTTCTTTTTGTTTATTTGTTTTTATCCCTTTTAAGATCATGTAGACGTTGCCGCCGAGGAAGTTGCTATT

Reverse complement sequence

AATAGCAACTTCCTCGGCGGCAACGTCTACATGATCTTAAAAGGGATAAAAACAAATAAACAAAAAGAAAAGGCAGAAAAATAACAACAAATAAAATAAC[T/C]
AATTAAATCGGAAGATAGAGCTCAACTTTTGAAGAATTAACTTAAGAAAATAAACAGGTCAATTCGGAGTTCGGATGGAGGAGATATAACAATTGGAAGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	48.40%	3.00%	0.30%	48.35%	NA
All Indica	2759	24.00%	2.30%	0.47%	73.25%	NA
All Japonica	1512	94.30%	4.80%	0.00%	0.86%	NA
Aus	269	20.10%	0.00%	0.37%	79.55%	NA
Indica I	595	48.60%	0.20%	0.34%	50.92%	NA
Indica II	465	24.50%	5.40%	0.65%	69.46%	NA
Indica III	913	4.40%	2.60%	0.44%	92.55%	NA
Indica Intermediate	786	27.70%	1.80%	0.51%	69.97%	NA
Temperate Japonica	767	96.70%	3.00%	0.00%	0.26%	NA
Tropical Japonica	504	98.80%	0.00%	0.00%	1.19%	NA
Japonica Intermediate	241	77.20%	20.70%	0.00%	2.07%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	61.10%	4.40%	0.00%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412497804	A -> DEL	N	N	silent_mutation	Average:12.31; most accessible tissue: Callus, score: 80.708	N	N	N	N
vg0412497804	A -> G	LOC_Os04g22060.1	upstream_gene_variant ; 3218.0bp to feature; MODIFIER	silent_mutation	Average:12.31; most accessible tissue: Callus, score: 80.708	N	N	N	N
vg0412497804	A -> G	LOC_Os04g22070.1	upstream_gene_variant ; 577.0bp to feature; MODIFIER	silent_mutation	Average:12.31; most accessible tissue: Callus, score: 80.708	N	N	N	N
vg0412497804	A -> G	LOC_Os04g22080.1	downstream_gene_variant ; 3184.0bp to feature; MODIFIER	silent_mutation	Average:12.31; most accessible tissue: Callus, score: 80.708	N	N	N	N
vg0412497804	A -> G	LOC_Os04g22070-LOC_Os04g22080	intergenic_region ; MODIFIER	silent_mutation	Average:12.31; most accessible tissue: Callus, score: 80.708	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412497804	2.91E-06	2.91E-06	mr1760_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