Search for Variation information by Variation ID:

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

Detailed information for vg0220759001:

Variant ID: vg0220759001 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20759001
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TCGAGCCCAACCTGCCAAGGAAGACCGACGACCTATCTCATAGCACCGGCCATGGCTGGACTACTCGAGAAAAGGTTATTAATGGATAATTCCTCGCGAA[C/T]
GTCGTCGGCTTGATCACCCGATATGATTGCGAACGGACATCCGGATATGCTATAAGTTGGGTATGTGAGTTATGCTGGCCACATGATATGCACATATAAT

Reverse complement sequence

ATTATATGTGCATATCATGTGGCCAGCATAACTCACATACCCAACTTATAGCATATCCGGATGTCCGTTCGCAATCATATCGGGTGATCAAGCCGACGAC[G/A]
TTCGCGAGGAATTATCCATTAATAACCTTTTCTCGAGTAGTCCAGCCATGGCCGGTGCTATGAGATAGGTCGTCGGTCTTCCTTGGCAGGTTGGGCTCGA

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	68.50%	31.10%	0.25%	0.21%	NA
All Indica	2759	49.00%	50.40%	0.29%	0.36%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	77.30%	21.90%	0.74%	0.00%	NA
Indica I	595	72.80%	26.70%	0.34%	0.17%	NA
Indica II	465	64.30%	34.80%	0.00%	0.86%	NA
Indica III	913	29.10%	70.20%	0.33%	0.33%	NA
Indica Intermediate	786	44.90%	54.50%	0.38%	0.25%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	84.40%	13.30%	2.22%	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
vg0220759001	C -> T	LOC_Os02g34620.1	downstream_gene_variant ; 12.0bp to feature; MODIFIER	silent_mutation	Average:48.874; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg0220759001	C -> T	LOC_Os02g34630.1	downstream_gene_variant ; 4323.0bp to feature; MODIFIER	silent_mutation	Average:48.874; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg0220759001	C -> T	LOC_Os02g34630.2	downstream_gene_variant ; 4323.0bp to feature; MODIFIER	silent_mutation	Average:48.874; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg0220759001	C -> T	LOC_Os02g34620-LOC_Os02g34630	intergenic_region ; MODIFIER	silent_mutation	Average:48.874; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N
vg0220759001	C -> DEL	N	N	silent_mutation	Average:48.874; most accessible tissue: Minghui63 root, score: 63.193	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220759001	2.38E-06	NA	mr1868	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
vg0220759001	9.78E-06	NA	mr1099_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
vg0220759001	NA	6.92E-06	mr1099_2	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