Search for Variation information by Variation ID:

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

Detailed information for vg0313718302:

Variant ID: vg0313718302 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 13718302
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCCTCCATTTGGCTTGAAAATGATAAAATAATGGTCACGTTGTCTTTTAGCAAATTACTATCATCTATTTTATATGACCTTGAGTGTGTCACATCTTT[G/A]
CAGTGTCCAAACTAAAAATTACAAACTTTAAGTGTCATGTAGTAAATTTTGCTATTTAAGTTTCATTTGTTGCACTACACCTGTAGATGAACATTAAAGT

Reverse complement sequence

ACTTTAATGTTCATCTACAGGTGTAGTGCAACAAATGAAACTTAAATAGCAAAATTTACTACATGACACTTAAAGTTTGTAATTTTTAGTTTGGACACTG[C/T]
AAAGATGTGACACACTCAAGGTCATATAAAATAGATGATAGTAATTTGCTAAAAGACAACGTGACCATTATTTTATCATTTTCAAGCCAAATGGAGGAAA

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	50.50%	49.40%	0.06%	0.00%	NA
All Indica	2759	19.10%	80.80%	0.07%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	79.90%	19.70%	0.37%	0.00%	NA
Indica I	595	23.40%	76.60%	0.00%	0.00%	NA
Indica II	465	49.70%	50.30%	0.00%	0.00%	NA
Indica III	913	2.00%	98.00%	0.00%	0.00%	NA
Indica Intermediate	786	17.80%	81.90%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	63.30%	36.70%	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
vg0313718302	G -> A	LOC_Os03g24170.1	upstream_gene_variant ; 1514.0bp to feature; MODIFIER	silent_mutation	Average:37.941; most accessible tissue: Callus, score: 77.636	N	N	N	N
vg0313718302	G -> A	LOC_Os03g24160.1	downstream_gene_variant ; 1544.0bp to feature; MODIFIER	silent_mutation	Average:37.941; most accessible tissue: Callus, score: 77.636	N	N	N	N
vg0313718302	G -> A	LOC_Os03g24160-LOC_Os03g24170	intergenic_region ; MODIFIER	silent_mutation	Average:37.941; most accessible tissue: Callus, score: 77.636	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0313718302	NA	1.62E-06	mr1024	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