Search for Variation information by Variation ID:

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

Detailed information for vg0125055810:

Variant ID: vg0125055810 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 25055810
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

CCCACATTCACATATGCTAGAAAGTCTTATAACCTGGAATGGAGGTAGTACAATTTTGATGAAGTTGCAAAATATTCGTTTTGCTATATTTTTAAAGTGT[C/T]
GATTCAATCAAACCAAATATTTGACAATACCTTTTCTTTACAAACTAAATGGAGAATTAATTTATTGATATGGCTAAATTATTTTTTGGTGGCATGGTTG

Reverse complement sequence

CAACCATGCCACCAAAAAATAATTTAGCCATATCAATAAATTAATTCTCCATTTAGTTTGTAAAGAAAAGGTATTGTCAAATATTTGGTTTGATTGAATC[G/A]
ACACTTTAAAAATATAGCAAAACGAATATTTTGCAACTTCATCAAAATTGTACTACCTCCATTCCAGGTTATAAGACTTTCTAGCATATGTGAATGTGGG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	86.90%	12.90%	0.17%	0.00%	NA
All Indica	2759	89.70%	10.00%	0.29%	0.00%	NA
All Japonica	1512	97.10%	2.90%	0.00%	0.00%	NA
Aus	269	19.00%	81.00%	0.00%	0.00%	NA
Indica I	595	78.20%	21.00%	0.84%	0.00%	NA
Indica II	465	96.60%	3.40%	0.00%	0.00%	NA
Indica III	913	94.30%	5.70%	0.00%	0.00%	NA
Indica Intermediate	786	89.10%	10.60%	0.38%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	97.10%	2.90%	0.00%	0.00%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0125055810	C -> T	LOC_Os01g43720.1	3_prime_UTR_variant ; 738.0bp to feature; MODIFIER	silent_mutation	Average:64.614; most accessible tissue: Callus, score: 92.843	N	N	N	N
vg0125055810	C -> T	LOC_Os01g43740.1	upstream_gene_variant ; 4954.0bp to feature; MODIFIER	silent_mutation	Average:64.614; most accessible tissue: Callus, score: 92.843	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0125055810	NA	1.37E-07	mr1662	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