Search for Variation information by Variation ID:

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

Detailed information for vg0523612364:

Variant ID: vg0523612364 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 23612364
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.66, T: 0.34, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

TAATATAAGAGATTTTGAGTTTTTGCTTGCACTGTTTGACCACTCGTCTTATTTAAAAAATTTGTGCAAATATAAAAAACGAAAAGTTGTGCTTAAAGTA[T/C]
TTTGGATAATAAAGTAAGTCACGAAAAAAATAAATAATAATTTCAAAATGTTTTGAATAAGACGAGTGGTCAAACAGTGCAAGAAAAAACTCAAAATCTC

Reverse complement sequence

GAGATTTTGAGTTTTTTCTTGCACTGTTTGACCACTCGTCTTATTCAAAACATTTTGAAATTATTATTTATTTTTTTCGTGACTTACTTTATTATCCAAA[A/G]
TACTTTAAGCACAACTTTTCGTTTTTTATATTTGCACAAATTTTTTAAATAAGACGAGTGGTCAAACAGTGCAAGCAAAAACTCAAAATCTCTTATATTA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.00%	28.80%	0.23%	0.00%	NA
All Indica	2759	58.60%	41.00%	0.40%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	33.80%	66.20%	0.00%	0.00%	NA
Indica I	595	49.20%	50.30%	0.50%	0.00%	NA
Indica II	465	54.00%	45.20%	0.86%	0.00%	NA
Indica III	913	66.50%	33.50%	0.00%	0.00%	NA
Indica Intermediate	786	59.40%	40.10%	0.51%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	65.60%	34.40%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	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
vg0523612364	T -> C	LOC_Os05g40200.1	upstream_gene_variant ; 1358.0bp to feature; MODIFIER	silent_mutation	Average:49.935; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N
vg0523612364	T -> C	LOC_Os05g40200-LOC_Os05g40212	intergenic_region ; MODIFIER	silent_mutation	Average:49.935; most accessible tissue: Zhenshan97 panicle, score: 74.671	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0523612364	3.47E-07	1.31E-07	mr1657	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
vg0523612364	NA	8.22E-06	mr1193_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