Search for Variation information by Variation ID:

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

Detailed information for vg1204375858:

Variant ID: vg1204375858 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4375858
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 54. )

Flanking Sequence (100 bp) in Reference Genome:

AACATGTTGATCCTATATTGCAAATGCTCCATTGTTTTTCTTCAAATACTGCATTGTTTTATAATATCACCATGGGATGTTTACCTACTGTCATAGCCAT[G/A]
CTATCTTGTACCATGTTCCTTTGTTAGCTTGGGATATAACATGACTAGAGATTGGACTAGGGAATGCTTAGCTTTGCTTAGTTCAACTAGCACACAATGG

Reverse complement sequence

CCATTGTGTGCTAGTTGAACTAAGCAAAGCTAAGCATTCCCTAGTCCAATCTCTAGTCATGTTATATCCCAAGCTAACAAAGGAACATGGTACAAGATAG[C/T]
ATGGCTATGACAGTAGGTAAACATCCCATGGTGATATTATAAAACAATGCAGTATTTGAAGAAAAACAATGGAGCATTTGCAATATAGGATCAACATGTT

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	34.20%	20.40%	20.72%	24.69%	NA
All Indica	2759	21.90%	31.00%	27.87%	19.25%	NA
All Japonica	1512	57.70%	0.50%	6.75%	35.12%	NA
Aus	269	29.70%	31.20%	25.65%	13.38%	NA
Indica I	595	32.80%	26.20%	34.62%	6.39%	NA
Indica II	465	30.80%	6.50%	19.78%	43.01%	NA
Indica III	913	6.40%	49.20%	29.46%	15.01%	NA
Indica Intermediate	786	26.50%	28.00%	25.70%	19.85%	NA
Temperate Japonica	767	80.80%	0.00%	7.69%	11.47%	NA
Tropical Japonica	504	32.10%	0.60%	5.56%	61.71%	NA
Japonica Intermediate	241	37.30%	1.70%	6.22%	54.77%	NA
VI/Aromatic	96	21.90%	7.30%	17.71%	53.12%	NA
Intermediate	90	42.20%	13.30%	24.44%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204375858	G -> DEL	N	N	silent_mutation	Average:5.821; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1204375858	G -> A	LOC_Os12g08600.1	upstream_gene_variant ; 994.0bp to feature; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1204375858	G -> A	LOC_Os12g08610.1	upstream_gene_variant ; 362.0bp to feature; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1204375858	G -> A	LOC_Os12g08620.1	upstream_gene_variant ; 3112.0bp to feature; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1204375858	G -> A	LOC_Os12g08600-LOC_Os12g08610	intergenic_region ; MODIFIER	silent_mutation	Average:5.821; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204375858	3.92E-06	3.92E-06	mr1196_2	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