Search for Variation information by Variation ID:

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

Detailed information for vg0809487809:

Variant ID: vg0809487809 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 9487809
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATATTTCATGCCTATACCTATCTCTAGTAATTTTTTCATGAATTTATAAAACTTTTAGAAATGGTTTTTACGGGTTTTCACTTATTTGATGGTTTTTACC[G/A]
GATATGTCCCCCTTCAAAATTATTGCCAAATTAACAAATACAACTCCAAACAACTATGAGCTAATAACCAGAACAAATTACCCAATGAGACTAACTAATA

Reverse complement sequence

TATTAGTTAGTCTCATTGGGTAATTTGTTCTGGTTATTAGCTCATAGTTGTTTGGAGTTGTATTTGTTAATTTGGCAATAATTTTGAAGGGGGACATATC[C/T]
GGTAAAAACCATCAAATAAGTGAAAACCCGTAAAAACCATTTCTAAAAGTTTTATAAATTCATGAAAAAATTACTAGAGATAGGTATAGGCATGAAATAT

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	96.60%	3.00%	0.36%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	90.10%	8.90%	1.06%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.10%	0.70%	0.26%	0.00%	NA
Tropical Japonica	504	88.90%	9.10%	1.98%	0.00%	NA
Japonica Intermediate	241	63.90%	34.40%	1.66%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0809487809	G -> A	LOC_Os08g15620.1	upstream_gene_variant ; 1521.0bp to feature; MODIFIER	silent_mutation	Average:29.791; most accessible tissue: Callus, score: 73.276	N	N	N	N
vg0809487809	G -> A	LOC_Os08g15610.1	downstream_gene_variant ; 2693.0bp to feature; MODIFIER	silent_mutation	Average:29.791; most accessible tissue: Callus, score: 73.276	N	N	N	N
vg0809487809	G -> A	LOC_Os08g15620-LOC_Os08g15630	intergenic_region ; MODIFIER	silent_mutation	Average:29.791; most accessible tissue: Callus, score: 73.276	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0809487809	NA	2.64E-06	mr1911	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
vg0809487809	1.69E-06	1.69E-06	mr1929	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