Search for Variation information by Variation ID:

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

Detailed information for vg0528732432:

Variant ID: vg0528732432 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 28732432
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

CTAATATTAGATAACAACTAATCGGATAGCCATATATAAAATTAAATCAAGATGAGTCTTCTCTATATGAAAATGTGAATAACATAAGTCTTCTCTACAC[G/A]
AAAATGTGAATAACATAAGTCCTATCTATATGAGAATGTGAATAACATATTTCATGAAAAATATGCTTTTATTTATTTTAGAAAATAATATGGTATTTTT

Reverse complement sequence

AAAAATACCATATTATTTTCTAAAATAAATAAAAGCATATTTTTCATGAAATATGTTATTCACATTCTCATATAGATAGGACTTATGTTATTCACATTTT[C/T]
GTGTAGAGAAGACTTATGTTATTCACATTTTCATATAGAGAAGACTCATCTTGATTTAATTTTATATATGGCTATCCGATTAGTTGTTATCTAATATTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	67.80%	32.10%	0.11%	0.00%	NA
All Indica	2759	96.20%	3.80%	0.04%	0.00%	NA
All Japonica	1512	12.50%	87.40%	0.13%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	94.80%	5.20%	0.00%	0.00%	NA
Indica II	465	93.80%	6.20%	0.00%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	5.00%	0.00%	0.00%	NA
Temperate Japonica	767	0.80%	99.20%	0.00%	0.00%	NA
Tropical Japonica	504	34.30%	65.70%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.00%	0.83%	0.00%	NA
VI/Aromatic	96	47.90%	52.10%	0.00%	0.00%	NA
Intermediate	90	54.40%	43.30%	2.22%	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
vg0528732432	G -> A	LOC_Os05g50140.1	downstream_gene_variant ; 2612.0bp to feature; MODIFIER	silent_mutation	Average:28.008; most accessible tissue: Callus, score: 69.317	N	N	N	N
vg0528732432	G -> A	LOC_Os05g50140.2	downstream_gene_variant ; 2979.0bp to feature; MODIFIER	silent_mutation	Average:28.008; most accessible tissue: Callus, score: 69.317	N	N	N	N
vg0528732432	G -> A	LOC_Os05g50130.1	intron_variant ; MODIFIER	silent_mutation	Average:28.008; most accessible tissue: Callus, score: 69.317	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0528732432	3.80E-07	1.87E-07	mr1409	Ind_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