Search for Variation information by Variation ID:

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

Detailed information for vg0431516011:

Variant ID: vg0431516011 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31516011
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTGTTTTATTACTGTAACTTGATTTATCATCTTGAAACATTATTACTTAATATTTTATATTTATAAAAAACAAAATAAATGGTCAAACGTTTGTTAAAAA[G/A]
TCAACGATGTTATATATTAAAAAAACAGAGGTAGTAACTTTTAAAGTTTAAATTTTATTTAAAATATAATAATTTTTTCACTTTTCACATATATTTTCTT

Reverse complement sequence

AAGAAAATATATGTGAAAAGTGAAAAAATTATTATATTTTAAATAAAATTTAAACTTTAAAAGTTACTACCTCTGTTTTTTTAATATATAACATCGTTGA[C/T]
TTTTTAACAAACGTTTGACCATTTATTTTGTTTTTTATAAATATAAAATATTAAGTAATAATGTTTCAAGATGATAAATCAAGTTACAGTAATAAAACAA

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	92.00%	5.70%	0.17%	2.18%	NA
All Indica	2759	95.60%	1.70%	0.14%	2.54%	NA
All Japonica	1512	86.20%	11.40%	0.20%	2.12%	NA
Aus	269	85.10%	14.90%	0.00%	0.00%	NA
Indica I	595	95.60%	1.30%	0.50%	2.52%	NA
Indica II	465	90.50%	7.10%	0.22%	2.15%	NA
Indica III	913	97.80%	0.00%	0.00%	2.19%	NA
Indica Intermediate	786	96.10%	0.80%	0.00%	3.18%	NA
Temperate Japonica	767	92.70%	2.90%	0.39%	4.04%	NA
Tropical Japonica	504	74.80%	25.00%	0.00%	0.20%	NA
Japonica Intermediate	241	89.60%	10.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	7.80%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0431516011	G -> DEL	N	N	silent_mutation	Average:44.62; most accessible tissue: Callus, score: 83.839	N	N	N	N
vg0431516011	G -> A	LOC_Os04g52900.1	upstream_gene_variant ; 1703.0bp to feature; MODIFIER	silent_mutation	Average:44.62; most accessible tissue: Callus, score: 83.839	N	N	N	N
vg0431516011	G -> A	LOC_Os04g52900.2	upstream_gene_variant ; 1703.0bp to feature; MODIFIER	silent_mutation	Average:44.62; most accessible tissue: Callus, score: 83.839	N	N	N	N
vg0431516011	G -> A	LOC_Os04g52910.1	downstream_gene_variant ; 3232.0bp to feature; MODIFIER	silent_mutation	Average:44.62; most accessible tissue: Callus, score: 83.839	N	N	N	N
vg0431516011	G -> A	LOC_Os04g52900-LOC_Os04g52910	intergenic_region ; MODIFIER	silent_mutation	Average:44.62; most accessible tissue: Callus, score: 83.839	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431516011	1.16E-06	NA	mr1083	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
vg0431516011	9.71E-07	NA	mr1226	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
vg0431516011	5.17E-07	NA	mr1233	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
vg0431516011	NA	1.78E-07	mr1233	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
vg0431516011	9.30E-07	NA	mr1411	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
vg0431516011	4.77E-06	NA	mr1800_2	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