Search for Variation information by Variation ID:

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

Detailed information for vg0427530535:

Variant ID: vg0427530535 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27530535
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.97, G: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAAGCATGAATACAAATGGAAGGGTGATTTTTCTGAAGTTTGAATCCTTCTTACAACTGGAAGTGTAGGACTACTTAGGGAAAACATTTTTTTTCTCT[A/G]
TAAATGCGGTGCTGCTTCATTTACTTTGGTATTATCGGATGATTCATTTCAGGAGACTGCATAATGTTTGCATAACATTCATTATTCCAATGCAAAACAA

Reverse complement sequence

TTGTTTTGCATTGGAATAATGAATGTTATGCAAACATTATGCAGTCTCCTGAAATGAATCATCCGATAATACCAAAGTAAATGAAGCAGCACCGCATTTA[T/C]
AGAGAAAAAAAATGTTTTCCCTAAGTAGTCCTACACTTCCAGTTGTAAGAAGGATTCAAACTTCAGAAAAATCACCCTTCCATTTGTATTCATGCTTTAA

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	81.40%	13.60%	4.89%	0.08%	NA
All Indica	2759	75.50%	16.60%	7.79%	0.11%	NA
All Japonica	1512	99.60%	0.30%	0.07%	0.00%	NA
Aus	269	30.90%	64.30%	4.46%	0.37%	NA
Indica I	595	99.50%	0.20%	0.34%	0.00%	NA
Indica II	465	32.70%	40.60%	26.02%	0.65%	NA
Indica III	913	84.60%	13.70%	1.75%	0.00%	NA
Indica Intermediate	786	72.30%	18.10%	9.67%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	6.70%	3.33%	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
vg0427530535	A -> DEL	N	N	silent_mutation	Average:24.088; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0427530535	A -> G	LOC_Os04g46430.1	upstream_gene_variant ; 246.0bp to feature; MODIFIER	silent_mutation	Average:24.088; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0427530535	A -> G	LOC_Os04g46420.1	downstream_gene_variant ; 4443.0bp to feature; MODIFIER	silent_mutation	Average:24.088; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N
vg0427530535	A -> G	LOC_Os04g46430-LOC_Os04g46440	intergenic_region ; MODIFIER	silent_mutation	Average:24.088; most accessible tissue: Zhenshan97 panicle, score: 36.038	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427530535	1.69E-06	1.69E-06	mr1848_2	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
vg0427530535	9.20E-06	9.20E-06	mr1848_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