Search for Variation information by Variation ID:

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

Detailed information for vg0630258758:

Variant ID: vg0630258758 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 30258758
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

GTATGTGCTGTTCTACAGGAGAATGATCTCTTTGGCTTAAATTTGTCTCAAAAGTCTTAAAATGCATGTCAGCTTTTAATCGGTCAACATATAAATGAGG[T/C]
TAAACTGGGTGTTTTTACTTACCGGCAGCGTACGTGTAACTTCGCGTCTTTACGAAATTTGGCTTATTAAGGGTTAGAAATTTGGCATGTTAAGGGTTAG

Reverse complement sequence

CTAACCCTTAACATGCCAAATTTCTAACCCTTAATAAGCCAAATTTCGTAAAGACGCGAAGTTACACGTACGCTGCCGGTAAGTAAAAACACCCAGTTTA[A/G]
CCTCATTTATATGTTGACCGATTAAAAGCTGACATGCATTTTAAGACTTTTGAGACAAATTTAAGCCAAAGAGATCATTCTCCTGTAGAACAGCACATAC

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	14.20%	9.90%	2.09%	73.78%	NA
All Indica	2759	0.70%	0.80%	0.65%	97.83%	NA
All Japonica	1512	42.30%	19.40%	4.10%	34.19%	NA
Aus	269	0.00%	50.90%	4.46%	44.61%	NA
Indica I	595	1.00%	0.00%	1.18%	97.82%	NA
Indica II	465	0.60%	0.60%	0.00%	98.71%	NA
Indica III	913	0.30%	0.20%	0.22%	99.23%	NA
Indica Intermediate	786	0.90%	2.30%	1.15%	95.67%	NA
Temperate Japonica	767	74.80%	16.70%	0.65%	7.82%	NA
Tropical Japonica	504	2.00%	25.80%	9.92%	62.30%	NA
Japonica Intermediate	241	23.20%	14.50%	2.90%	59.34%	NA
VI/Aromatic	96	1.00%	7.30%	4.17%	87.50%	NA
Intermediate	90	11.10%	11.10%	3.33%	74.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0630258758	T -> C	LOC_Os06g49960.1	upstream_gene_variant ; 3483.0bp to feature; MODIFIER	silent_mutation	Average:12.682; most accessible tissue: Callus, score: 82.481	N	N	N	N
vg0630258758	T -> C	LOC_Os06g49970.2	upstream_gene_variant ; 4020.0bp to feature; MODIFIER	silent_mutation	Average:12.682; most accessible tissue: Callus, score: 82.481	N	N	N	N
vg0630258758	T -> C	LOC_Os06g49960-LOC_Os06g49970	intergenic_region ; MODIFIER	silent_mutation	Average:12.682; most accessible tissue: Callus, score: 82.481	N	N	N	N
vg0630258758	T -> DEL	N	N	silent_mutation	Average:12.682; most accessible tissue: Callus, score: 82.481	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0630258758	6.29E-06	NA	mr1740	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