Search for Variation information by Variation ID:

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

Detailed information for vg0407833565:

Variant ID: vg0407833565 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 7833565
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.87, G: 0.15, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GAACCAATCCAATATATAAGTTTCATGCTAATCAAATTATAACCCATAGGAAAATAAAGTCATCTACAGCCATTAATTAATTGGGAAAGGTTCACCACCC[A/G]
ATGACATTCGAAAATAATGCATAGTTGAAATAAAATAATAGCTTTAAACGGGTTCAACATGCTCAAAAGGTTGTTTGGGATCTGTGTGACTTGCCTTGAG

Reverse complement sequence

CTCAAGGCAAGTCACACAGATCCCAAACAACCTTTTGAGCATGTTGAACCCGTTTAAAGCTATTATTTTATTTCAACTATGCATTATTTTCGAATGTCAT[T/C]
GGGTGGTGAACCTTTCCCAATTAATTAATGGCTGTAGATGACTTTATTTTCCTATGGGTTATAATTTGATTAGCATGAAACTTATATATTGGATTGGTTC

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	40.10%	3.30%	31.49%	25.10%	NA
All Indica	2759	10.70%	1.40%	46.10%	41.79%	NA
All Japonica	1512	98.70%	0.00%	0.60%	0.66%	NA
Aus	269	3.00%	43.50%	52.04%	1.49%	NA
Indica I	595	13.30%	0.30%	15.80%	70.59%	NA
Indica II	465	13.50%	0.60%	36.77%	49.03%	NA
Indica III	913	6.10%	2.10%	70.10%	21.69%	NA
Indica Intermediate	786	12.50%	1.80%	46.69%	39.06%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	97.60%	0.00%	1.39%	0.99%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	54.20%	0.00%	39.58%	6.25%	NA
Intermediate	90	52.20%	1.10%	32.22%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0407833565	A -> DEL	N	N	silent_mutation	Average:20.268; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0407833565	A -> G	LOC_Os04g14020.1	upstream_gene_variant ; 4549.0bp to feature; MODIFIER	silent_mutation	Average:20.268; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0407833565	A -> G	LOC_Os04g14040.1	upstream_gene_variant ; 395.0bp to feature; MODIFIER	silent_mutation	Average:20.268; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N
vg0407833565	A -> G	LOC_Os04g14020-LOC_Os04g14040	intergenic_region ; MODIFIER	silent_mutation	Average:20.268; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0407833565	2.07E-07	3.14E-08	mr1407	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
vg0407833565	3.90E-06	2.12E-07	mr1596	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