Search for Variation information by Variation ID:

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

Detailed information for vg0320043666:

Variant ID: vg0320043666 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20043666
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

CTAAGCAACTAATTTCTCCTCCAAATTATTGAGCTCACAAAAATCATCAAATTGAACATAGCTAAAAGTATTTAAAGAAGTTATCAATTTACGTTCCTCA[A/G]
CATCATTAGCAATGTGAACATCATGCTTAAAATCAGCACACAATGAAACACTAGAAATAGCATGTTCATTCACTAGTTGTGGTAGGGATATAAGTGAAGC

Reverse complement sequence

GCTTCACTTATATCCCTACCACAACTAGTGAATGAACATGCTATTTCTAGTGTTTCATTGTGTGCTGATTTTAAGCATGATGTTCACATTGCTAATGATG[T/C]
TGAGGAACGTAAATTGATAACTTCTTTAAATACTTTTAGCTATGTTCAATTTGATGATTTTTGTGAGCTCAATAATTTGGAGGAGAAATTAGTTGCTTAG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.10%	12.90%	4.72%	30.24%	NA
All Indica	2759	36.10%	20.80%	7.29%	35.81%	NA
All Japonica	1512	86.10%	0.00%	0.20%	13.69%	NA
Aus	269	12.60%	13.80%	3.72%	69.89%	NA
Indica I	595	58.20%	16.00%	10.92%	14.96%	NA
Indica II	465	36.60%	2.60%	4.73%	56.13%	NA
Indica III	913	18.90%	38.20%	5.37%	37.46%	NA
Indica Intermediate	786	39.20%	14.90%	8.27%	37.66%	NA
Temperate Japonica	767	99.60%	0.00%	0.13%	0.26%	NA
Tropical Japonica	504	66.30%	0.00%	0.40%	33.33%	NA
Japonica Intermediate	241	84.60%	0.00%	0.00%	15.35%	NA
VI/Aromatic	96	71.90%	0.00%	4.17%	23.96%	NA
Intermediate	90	66.70%	2.20%	5.56%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320043666	A -> DEL	LOC_Os03g36130.1	N	frameshift_variant	Average:9.414; most accessible tissue: Callus, score: 21.868	N	N	N	N
vg0320043666	A -> G	LOC_Os03g36130.1	missense_variant ; p.Val164Ala; MODERATE	nonsynonymous_codon ; V164A	Average:9.414; most accessible tissue: Callus, score: 21.868	benign	1.226	DELETERIOUS	0.04

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320043666	NA	1.09E-06	mr1519	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
vg0320043666	NA	1.84E-07	mr1045_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
vg0320043666	NA	2.10E-06	mr1105_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
vg0320043666	NA	4.04E-08	mr1218_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
vg0320043666	NA	1.62E-07	mr1232_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
vg0320043666	NA	9.70E-06	mr1391_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
vg0320043666	7.06E-06	1.18E-06	mr1421_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
vg0320043666	NA	5.45E-06	mr1422_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
vg0320043666	9.01E-06	NA	mr1510_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
vg0320043666	7.54E-08	NA	mr1519_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
vg0320043666	1.85E-09	5.10E-18	mr1519_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
vg0320043666	NA	5.37E-06	mr1562_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
vg0320043666	NA	6.20E-06	mr1566_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
vg0320043666	4.75E-06	4.74E-06	mr1752_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
vg0320043666	NA	2.04E-07	mr1825_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
vg0320043666	6.14E-07	NA	mr1874_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
vg0320043666	NA	1.44E-07	mr1874_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
vg0320043666	NA	1.89E-06	mr1901_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
vg0320043666	1.50E-06	1.49E-06	mr1953_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