Search for Variation information by Variation ID:

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

Detailed information for vg1124408117:

Variant ID: vg1124408117 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24408117
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TAAACTTTAGATGTATAGAAATACTATTTATAAAAAATATTTGAATTTAAATTCAAATTTGAATCGGATATAATTCAAATTCAAATTTGAATCGGGTATG[T/G]
AAACTTTTGACTTATAAACTTTGGGTTTATAAACTTTAGGTGTATAAACTTTAAATGCATAGAAATACTATATATAAAAAAATATTTGAATTTAAATTCA

Reverse complement sequence

TGAATTTAAATTCAAATATTTTTTTATATATAGTATTTCTATGCATTTAAAGTTTATACACCTAAAGTTTATAAACCCAAAGTTTATAAGTCAAAAGTTT[A/C]
CATACCCGATTCAAATTTGAATTTGAATTATATCCGATTCAAATTTGAATTTAAATTCAAATATTTTTTATAAATAGTATTTCTATACATCTAAAGTTTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	89.90%	8.50%	1.52%	0.08%	NA
All Indica	2759	84.00%	13.40%	2.50%	0.11%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	89.20%	9.70%	0.74%	0.37%	NA
Indica I	595	90.40%	6.10%	3.36%	0.17%	NA
Indica II	465	97.00%	1.70%	1.08%	0.22%	NA
Indica III	913	70.80%	25.60%	3.50%	0.11%	NA
Indica Intermediate	786	86.90%	11.60%	1.53%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	96.70%	2.20%	1.11%	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
vg1124408117	T -> DEL	N	N	silent_mutation	Average:14.832; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1124408117	T -> G	LOC_Os11g40790-LOC_Os11g40800	intergenic_region ; MODIFIER	silent_mutation	Average:14.832; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124408117	4.94E-06	4.93E-06	mr1370	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