Search for Variation information by Variation ID:

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

Detailed information for vg0402061955:

Variant ID: vg0402061955 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2061955
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 281. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGATGAAGCATGTGGTCAGCTAGCAATAAGCAAGAACAAATCGTACGAGGCTGAAATCGCTGCCTTGAAGAATCAAAATGCAGCCCTCCAGATGAAGA[T/C]
ACAAGCACTGGAGAATTACAGGCAGGCTAAGCACAAAGAGTATGCAGAACTGGAAACCATATATAAGAAGCTCAAAGCAAAGCACAGCAACTGTCGTTGA

Reverse complement sequence

TCAACGACAGTTGCTGTGCTTTGCTTTGAGCTTCTTATATATGGTTTCCAGTTCTGCATACTCTTTGTGCTTAGCCTGCCTGTAATTCTCCAGTGCTTGT[A/G]
TCTTCATCTGGAGGGCTGCATTTTGATTCTTCAAGGCAGCGATTTCAGCCTCGTACGATTTGTTCTTGCTTATTGCTAGCTGACCACATGCTTCATCCTG

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	87.10%	12.20%	0.72%	0.00%	NA
All Indica	2759	99.00%	0.90%	0.14%	0.00%	NA
All Japonica	1512	68.50%	30.90%	0.66%	0.00%	NA
Aus	269	94.40%	5.20%	0.37%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.40%	0.40%	0.22%	0.00%	NA
Indica III	913	98.20%	1.80%	0.00%	0.00%	NA
Indica Intermediate	786	98.90%	0.80%	0.38%	0.00%	NA
Temperate Japonica	767	72.40%	26.50%	1.17%	0.00%	NA
Tropical Japonica	504	74.40%	25.60%	0.00%	0.00%	NA
Japonica Intermediate	241	43.60%	56.00%	0.41%	0.00%	NA
VI/Aromatic	96	20.80%	59.40%	19.79%	0.00%	NA
Intermediate	90	85.60%	14.40%	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
vg0402061955	T -> C	LOC_Os04g04370.1	upstream_gene_variant ; 4071.0bp to feature; MODIFIER	silent_mutation	Average:51.499; most accessible tissue: Callus, score: 75.66	N	N	N	N
vg0402061955	T -> C	LOC_Os04g04380.1	downstream_gene_variant ; 4227.0bp to feature; MODIFIER	silent_mutation	Average:51.499; most accessible tissue: Callus, score: 75.66	N	N	N	N
vg0402061955	T -> C	LOC_Os04g04370-LOC_Os04g04380	intergenic_region ; MODIFIER	silent_mutation	Average:51.499; most accessible tissue: Callus, score: 75.66	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402061955	1.54E-07	NA	mr1670	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
vg0402061955	NA	1.71E-08	mr1691	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