Search for Variation information by Variation ID:

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

Detailed information for vg0208692453:

Variant ID: vg0208692453 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8692453
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.72, G: 0.28, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

TACGTGGGATTGATGGAGATAAATTTAATTGATCGTTTTTAAAAATAGATCTAATGGTTGGTAACAATGGGTCCATCGGGAATAAATTAAAAAAATCGAC[A/G]
GTTAGATGTTTTGTCTTCTTTTGATTTTTTTAGAAATAATTATAGTGTCACGTGGAGGCTTAGGAGCATTTGTAGGGTTGCTATGTGGCGGCTTAGGAGC

Reverse complement sequence

GCTCCTAAGCCGCCACATAGCAACCCTACAAATGCTCCTAAGCCTCCACGTGACACTATAATTATTTCTAAAAAAATCAAAAGAAGACAAAACATCTAAC[T/C]
GTCGATTTTTTTAATTTATTCCCGATGGACCCATTGTTACCAACCATTAGATCTATTTTTAAAAACGATCAATTAAATTTATCTCCATCAATCCCACGTA

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	44.80%	1.40%	5.01%	48.79%	NA
All Indica	2759	36.20%	1.90%	7.03%	54.80%	NA
All Japonica	1512	55.90%	0.40%	1.46%	42.26%	NA
Aus	269	72.90%	0.00%	2.97%	24.16%	NA
Indica I	595	34.50%	0.00%	7.06%	58.49%	NA
Indica II	465	43.90%	1.10%	5.81%	49.25%	NA
Indica III	913	32.60%	3.00%	8.21%	56.19%	NA
Indica Intermediate	786	37.30%	2.70%	6.36%	53.69%	NA
Temperate Japonica	767	80.60%	0.10%	0.39%	18.90%	NA
Tropical Japonica	504	28.80%	0.60%	2.98%	67.66%	NA
Japonica Intermediate	241	34.00%	0.80%	1.66%	63.49%	NA
VI/Aromatic	96	26.00%	6.20%	6.25%	61.46%	NA
Intermediate	90	56.70%	1.10%	7.78%	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
vg0208692453	A -> G	LOC_Os02g15510.1	downstream_gene_variant ; 1566.0bp to feature; MODIFIER	silent_mutation	Average:14.664; most accessible tissue: Callus, score: 32.486	N	N	N	N
vg0208692453	A -> G	LOC_Os02g15500-LOC_Os02g15510	intergenic_region ; MODIFIER	silent_mutation	Average:14.664; most accessible tissue: Callus, score: 32.486	N	N	N	N
vg0208692453	A -> DEL	N	N	silent_mutation	Average:14.664; most accessible tissue: Callus, score: 32.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208692453	1.75E-06	6.34E-08	mr1786_2	Jap_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