Search for Variation information by Variation ID:

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

Detailed information for vg0302880485:

Variant ID: vg0302880485 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 2880485
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.02, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTCAGCATGGCGGGCCAGCCGCAACAGTAGACGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGATGCCGCGCTGCTAGCTGAGCCGTTCGCACGG[C/T]
GGCCTGATCGAGCGCGCATTGCCATTTATCGTTTTTGATTTTCTCACTCTCTCTCTCGCCTGTTTGTAGAAGGGACGAGCATACTACTACCGCTAATTAC

Reverse complement sequence

GTAATTAGCGGTAGTAGTATGCTCGTCCCTTCTACAAACAGGCGAGAGAGAGAGTGAGAAAATCAAAAACGATAAATGGCAATGCGCGCTCGATCAGGCC[G/A]
CCGTGCGAACGGCTCAGCTAGCAGCGCGGCATCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCGTCTACTGTTGCGGCTGGCCCGCCATGCTGAAGG

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	60.40%	39.00%	0.34%	0.21%	NA
All Indica	2759	95.90%	3.50%	0.43%	0.14%	NA
All Japonica	1512	0.30%	99.50%	0.00%	0.20%	NA
Aus	269	48.70%	51.30%	0.00%	0.00%	NA
Indica I	595	98.00%	1.30%	0.50%	0.17%	NA
Indica II	465	93.50%	5.80%	0.43%	0.22%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	91.70%	7.30%	0.76%	0.25%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.20%	99.60%	0.00%	0.20%	NA
Japonica Intermediate	241	0.80%	98.30%	0.00%	0.83%	NA
VI/Aromatic	96	35.40%	63.50%	0.00%	1.04%	NA
Intermediate	90	43.30%	50.00%	4.44%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0302880485	C -> T	LOC_Os03g05770.1	3_prime_UTR_variant ; 69.0bp to feature; MODIFIER	silent_mutation	Average:62.736; most accessible tissue: Callus, score: 83.477	N	N	N	N
vg0302880485	C -> T	LOC_Os03g05780.1	downstream_gene_variant ; 2520.0bp to feature; MODIFIER	silent_mutation	Average:62.736; most accessible tissue: Callus, score: 83.477	N	N	N	N
vg0302880485	C -> DEL	N	N	silent_mutation	Average:62.736; most accessible tissue: Callus, score: 83.477	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0302880485	NA	5.21E-48	mr1063	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
vg0302880485	NA	8.08E-15	mr1870	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
vg0302880485	NA	2.87E-37	mr1129_2	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
vg0302880485	NA	5.00E-21	mr1255_2	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