Search for Variation information by Variation ID:

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

Detailed information for vg0427867420:

Variant ID: vg0427867420 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 27867420
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.90, T: 0.10, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TCCGTTCCATAATATAAAGGATTATGACCTTTTACTTGTACTGTTTGACCACTCGTCTTATTAAAAAAAATTATGCAAATATAAAAAATGAAAAGTTGCG[T/C]
TTAAAGTACTTTGGATAATAAAGCCAGTCACAAATAAAATAAATAATAATTCTAAATTATTTTTGAATAATATAAAATCCTAAAATATAACACTTTTTAG

Reverse complement sequence

CTAAAAAGTGTTATATTTTAGGATTTTATATTATTCAAAAATAATTTAGAATTATTATTTATTTTATTTGTGACTGGCTTTATTATCCAAAGTACTTTAA[A/G]
CGCAACTTTTCATTTTTTATATTTGCATAATTTTTTTTAATAAGACGAGTGGTCAAACAGTACAAGTAAAAGGTCATAATCCTTTATATTATGGAACGGA

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	51.40%	48.40%	0.25%	0.00%	NA
All Indica	2759	80.70%	18.80%	0.43%	0.00%	NA
All Japonica	1512	0.50%	99.50%	0.00%	0.00%	NA
Aus	269	59.10%	40.90%	0.00%	0.00%	NA
Indica I	595	80.50%	19.20%	0.34%	0.00%	NA
Indica II	465	91.60%	8.00%	0.43%	0.00%	NA
Indica III	913	76.90%	22.70%	0.44%	0.00%	NA
Indica Intermediate	786	78.90%	20.60%	0.51%	0.00%	NA
Temperate Japonica	767	0.40%	99.60%	0.00%	0.00%	NA
Tropical Japonica	504	0.60%	99.40%	0.00%	0.00%	NA
Japonica Intermediate	241	0.80%	99.20%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	36.70%	63.30%	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
vg0427867420	T -> C	LOC_Os04g47010.1	upstream_gene_variant ; 835.0bp to feature; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0427867420	T -> C	LOC_Os04g47020.1	upstream_gene_variant ; 664.0bp to feature; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0427867420	T -> C	LOC_Os04g47020.2	upstream_gene_variant ; 658.0bp to feature; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0427867420	T -> C	LOC_Os04g47020.3	upstream_gene_variant ; 664.0bp to feature; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0427867420	T -> C	LOC_Os04g47030.1	downstream_gene_variant ; 3729.0bp to feature; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0427867420	T -> C	LOC_Os04g47010-LOC_Os04g47020	intergenic_region ; MODIFIER	silent_mutation	Average:53.684; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0427867420	7.61E-07	NA	mr1873	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
vg0427867420	1.53E-06	2.82E-07	mr1873	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
vg0427867420	NA	1.92E-15	mr1579_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
vg0427867420	NA	7.69E-08	mr1690_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
vg0427867420	2.60E-06	2.56E-36	mr1873_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
vg0427867420	5.81E-07	1.65E-08	mr1873_2	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