Search for Variation information by Variation ID:

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

Detailed information for vg0623902712:

Variant ID: vg0623902712 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 23902712
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGCAAGGTAGCACGCCCGTACACAACATACACAACATATACACCTGCAGATAATCCCCTATATATAAATTTCTGATCTGTATACTCTCAGCATTTATACT[G/A]
ACACTACAGTTATTGATGATGATGATGATTAAATCTCATTTTCTGCAGGTTTCACATTTTTGCAGGTAAACGGTGGGGGCAAGTCCGAGTTGGGCGGCTT

Reverse complement sequence

AAGCCGCCCAACTCGGACTTGCCCCCACCGTTTACCTGCAAAAATGTGAAACCTGCAGAAAATGAGATTTAATCATCATCATCATCAATAACTGTAGTGT[C/T]
AGTATAAATGCTGAGAGTATACAGATCAGAAATTTATATATAGGGGATTATCTGCAGGTGTATATGTTGTGTATGTTGTGTACGGGCGTGCTACCTTGCA

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	98.30%	1.40%	0.30%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.80%	4.30%	0.93%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	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	90.20%	8.00%	1.83%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0623902712	G -> A	LOC_Os06g40150.1	upstream_gene_variant ; 2882.0bp to feature; MODIFIER	silent_mutation	Average:72.964; most accessible tissue: Zhenshan97 flower, score: 88.978	N	N	N	N
vg0623902712	G -> A	LOC_Os06g40160.1	intron_variant ; MODIFIER	silent_mutation	Average:72.964; most accessible tissue: Zhenshan97 flower, score: 88.978	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0623902712	NA	8.33E-06	mr1535	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
vg0623902712	1.07E-06	1.07E-06	mr1950	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