Search for Variation information by Variation ID:

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

Detailed information for vg0226490001:

Variant ID: vg0226490001 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26490001
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.96, T: 0.03, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGATGGAATGACAAGACCACCAGTTGTCGCTCCCTTGGAAATATGTCAATCTGGCAGGAGGGTGTTCTATGTCTTGTCATAATTGCTCTTTGTGGTTT[C/T]
GTAGCAGGAATGTGCTATCGGTTTAGCTATGCCATTGCCTTCATGATAATAGCTCTTCTCATAGCTGTTGCTGCTGGTTTTGCTCTCCAGTTTCGACAGG

Reverse complement sequence

CCTGTCGAAACTGGAGAGCAAAACCAGCAGCAACAGCTATGAGAAGAGCTATTATCATGAAGGCAATGGCATAGCTAAACCGATAGCACATTCCTGCTAC[G/A]
AAACCACAAAGAGCAATTATGACAAGACATAGAACACCCTCCTGCCAGATTGACATATTTCCAAGGGAGCGACAACTGGTGGTCTTGTCATTCCATCGAA

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	55.90%	44.10%	0.02%	0.00%	NA
All Indica	2759	31.30%	68.70%	0.04%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	43.90%	56.10%	0.00%	0.00%	NA
Indica I	595	15.60%	84.40%	0.00%	0.00%	NA
Indica II	465	25.20%	74.80%	0.00%	0.00%	NA
Indica III	913	48.30%	51.70%	0.00%	0.00%	NA
Indica Intermediate	786	27.00%	72.90%	0.13%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	70.00%	30.00%	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
vg0226490001	C -> T	LOC_Os02g43860.1	synonymous_variant ; p.Phe492Phe; LOW	synonymous_codon	Average:66.754; most accessible tissue: Callus, score: 90.024	N	N	N	N
vg0226490001	C -> T	LOC_Os02g43860.2	synonymous_variant ; p.Phe492Phe; LOW	synonymous_codon	Average:66.754; most accessible tissue: Callus, score: 90.024	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226490001	NA	4.42E-15	mr1592	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
vg0226490001	NA	5.04E-06	mr1074_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
vg0226490001	NA	2.73E-15	mr1148_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
vg0226490001	NA	6.23E-06	mr1148_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
vg0226490001	NA	5.08E-06	mr1150_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
vg0226490001	NA	9.73E-09	mr1198_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
vg0226490001	NA	7.01E-09	mr1222_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
vg0226490001	NA	2.67E-07	mr1227_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
vg0226490001	4.88E-06	2.61E-06	mr1918_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