Search for Variation information by Variation ID:

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

Detailed information for vg0432443771:

Variant ID: vg0432443771 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 32443771
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.29, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

AACATCCAAAAACGATATTTTTTTTTCACTTTTAAACCTTTTTTATTTTAAAAATAAATTCATCAAAAATTTATTTTAAAGTTAAACATTTTGTCCATAT[C/T]
AACCTACCTGGCATGGCAAGACAACACTGACATATCATCTACAACGAGCGTGATAGTTTTATCCTAACATGTCAATGTAAGACAATGTCTTCACGCTATT

Reverse complement sequence

AATAGCGTGAAGACATTGTCTTACATTGACATGTTAGGATAAAACTATCACGCTCGTTGTAGATGATATGTCAGTGTTGTCTTGCCATGCCAGGTAGGTT[G/A]
ATATGGACAAAATGTTTAACTTTAAAATAAATTTTTGATGAATTTATTTTTAAAATAAAAAAGGTTTAAAAGTGAAAAAAAAATATCGTTTTTGGATGTT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	51.70%	48.20%	0.02%	0.00%	NA
All Indica	2759	32.30%	67.70%	0.04%	0.00%	NA
All Japonica	1512	75.90%	24.10%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	17.50%	82.50%	0.00%	0.00%	NA
Indica II	465	27.30%	72.70%	0.00%	0.00%	NA
Indica III	913	49.80%	50.10%	0.11%	0.00%	NA
Indica Intermediate	786	26.00%	74.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	35.50%	64.50%	0.00%	0.00%	NA
Japonica Intermediate	241	90.90%	9.10%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	54.40%	45.60%	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
vg0432443771	C -> T	LOC_Os04g54540.1	upstream_gene_variant ; 4293.0bp to feature; MODIFIER	silent_mutation	Average:48.912; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443771	C -> T	LOC_Os04g54550.1	downstream_gene_variant ; 1627.0bp to feature; MODIFIER	silent_mutation	Average:48.912; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443771	C -> T	LOC_Os04g54560.1	downstream_gene_variant ; 4719.0bp to feature; MODIFIER	silent_mutation	Average:48.912; most accessible tissue: Callus, score: 79.272	N	N	N	N
vg0432443771	C -> T	LOC_Os04g54540-LOC_Os04g54550	intergenic_region ; MODIFIER	silent_mutation	Average:48.912; most accessible tissue: Callus, score: 79.272	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0432443771	NA	1.34E-07	mr1229	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
vg0432443771	2.14E-06	1.11E-12	mr1403	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
vg0432443771	7.27E-07	NA	mr1800	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
vg0432443771	4.30E-07	3.00E-09	mr1800	Ind_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
vg0432443771	NA	8.56E-06	mr1388_2	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
vg0432443771	8.64E-11	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
vg0432443771	3.17E-09	8.39E-12	mr1800_2	Ind_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