Search for Variation information by Variation ID:

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

Detailed information for vg1118908807:

Variant ID: vg1118908807 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18908807
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTGGATCCTAATTTGAGAGGAAGGCCACGTTCTAAACTAACTGACTTGTTTCCCGTTAGCAGTTAGCACGTTTTCCAAACTGTTAAATACTATATAAGAC[T/G]
GCTAACTGTTCGTTTTTTTTAAAAAAAATACATATAAAAGTTTTTAAAAAACAAACAAATCATTTTTCTAAAATTTATAATAATAGTTATTAATATTTAA

Reverse complement sequence

TTAAATATTAATAACTATTATTATAAATTTTAGAAAAATGATTTGTTTGTTTTTTAAAAACTTTTATATGTATTTTTTTTAAAAAAAACGAACAGTTAGC[A/C]
GTCTTATATAGTATTTAACAGTTTGGAAAACGTGCTAACTGCTAACGGGAAACAAGTCAGTTAGTTTAGAACGTGGCCTTCCTCTCAAATTAGGATCCAG

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	85.50%	11.40%	3.15%	0.00%	NA
All Indica	2759	99.50%	0.40%	0.14%	0.00%	NA
All Japonica	1512	59.10%	31.80%	9.06%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	99.00%	0.60%	0.38%	0.00%	NA
Temperate Japonica	767	72.50%	15.50%	11.99%	0.00%	NA
Tropical Japonica	504	40.10%	54.80%	5.16%	0.00%	NA
Japonica Intermediate	241	56.40%	35.70%	7.88%	0.00%	NA
VI/Aromatic	96	60.40%	35.40%	4.17%	0.00%	NA
Intermediate	90	84.40%	11.10%	4.44%	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
vg1118908807	T -> G	LOC_Os11g32090.1	upstream_gene_variant ; 4260.0bp to feature; MODIFIER	silent_mutation	Average:40.327; most accessible tissue: Callus, score: 65.502	N	N	N	N
vg1118908807	T -> G	LOC_Os11g32090-LOC_Os11g32100	intergenic_region ; MODIFIER	silent_mutation	Average:40.327; most accessible tissue: Callus, score: 65.502	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118908807	4.77E-06	NA	mr1141	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
vg1118908807	9.50E-06	NA	mr1241	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
vg1118908807	NA	1.54E-06	mr1404	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