Search for Variation information by Variation ID:

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

Detailed information for vg0516647020:

Variant ID: vg0516647020 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16647020
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AGTGCATGGAGCGCAACTCAGGGGTGACTGTGCAAAAGTTCAAGTCGACTCGATGAAGCCGGAATATGAGCTATTCCCACTAAAGTATCCACCGAATGAC[G/A]
AGGTCCTCTCACTAGGAAATGCCCGTGGTACCTTCATCCAATGGCCCAAAGACCTCATTGAGATCAAGATTACAGCGAGGCCAACCACTGCACCAGGCGG

Reverse complement sequence

CCGCCTGGTGCAGTGGTTGGCCTCGCTGTAATCTTGATCTCAATGAGGTCTTTGGGCCATTGGATGAAGGTACCACGGGCATTTCCTAGTGAGAGGACCT[C/T]
GTCATTCGGTGGATACTTTAGTGGGAATAGCTCATATTCCGGCTTCATCGAGTCGACTTGAACTTTTGCACAGTCACCCCTGAGTTGCGCTCCATGCACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.60%	28.40%	0.08%	0.00%	NA
All Indica	2759	52.70%	47.20%	0.14%	0.00%	NA
All Japonica	1512	98.80%	1.20%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	45.00%	55.00%	0.00%	0.00%	NA
Indica II	465	73.50%	26.50%	0.00%	0.00%	NA
Indica III	913	46.90%	53.00%	0.11%	0.00%	NA
Indica Intermediate	786	52.90%	46.70%	0.38%	0.00%	NA
Temperate Japonica	767	98.20%	1.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0516647020	G -> A	LOC_Os05g28430.1	missense_variant ; p.Glu400Lys; MODERATE	nonsynonymous_codon ; E400K	Average:35.352; most accessible tissue: Zhenshan97 flag leaf, score: 68.703	benign	0.278	DELETERIOUS	0.03

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516647020	4.35E-06	4.35E-06	mr1273_2	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
vg0516647020	NA	6.61E-06	mr1355_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
vg0516647020	NA	9.52E-06	mr1360_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
vg0516647020	NA	3.01E-07	mr1499_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
vg0516647020	NA	5.61E-07	mr1499_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
vg0516647020	NA	6.18E-06	mr1645_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
vg0516647020	NA	4.24E-06	mr1647_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
vg0516647020	NA	5.89E-06	mr1648_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
vg0516647020	NA	2.29E-08	mr1655_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
vg0516647020	NA	3.56E-06	mr1655_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
vg0516647020	NA	1.45E-06	mr1669_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
vg0516647020	NA	4.06E-06	mr1669_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