Search for Variation information by Variation ID:

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

Detailed information for vg0408482568:

Variant ID: vg0408482568 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 8482568
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:

GAAGGAGAAGGATCAAGATCTTCCCTATCCTTTGGTTTTCCTTGGCTCACTGGAATGTCGTGTGCTCCTCTGTGACTGTGGCAGCAAGTTTGGTCTCACC[A/G]
TAAATCGTGGGGGGGGGGGGGATGGACCAGAGAAGAGGAGAGAAGGAAGAAGAGGCATGACATGTGGGCCAATGTTTTGTTTGATAGGATTGCCATGTGT

Reverse complement sequence

ACACATGGCAATCCTATCAAACAAAACATTGGCCCACATGTCATGCCTCTTCTTCCTTCTCTCCTCTTCTCTGGTCCATCCCCCCCCCCCCCACGATTTA[T/C]
GGTGAGACCAAACTTGCTGCCACAGTCACAGAGGAGCACACGACATTCCAGTGAGCCAAGGAAAACCAAAGGATAGGGAAGATCTTGATCCTTCTCCTTC

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	62.00%	29.80%	5.95%	2.35%	NA
All Indica	2759	49.80%	44.40%	3.81%	1.92%	NA
All Japonica	1512	83.90%	1.30%	10.98%	3.84%	NA
Aus	269	52.40%	47.60%	0.00%	0.00%	NA
Indica I	595	64.40%	22.70%	11.60%	1.34%	NA
Indica II	465	46.70%	50.30%	2.58%	0.43%	NA
Indica III	913	44.40%	52.60%	0.33%	2.74%	NA
Indica Intermediate	786	47.10%	48.00%	2.67%	2.29%	NA
Temperate Japonica	767	87.10%	0.40%	10.69%	1.83%	NA
Tropical Japonica	504	78.40%	2.60%	11.71%	7.34%	NA
Japonica Intermediate	241	85.10%	1.70%	10.37%	2.90%	NA
VI/Aromatic	96	95.80%	3.10%	1.04%	0.00%	NA
Intermediate	90	57.80%	32.20%	10.00%	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
vg0408482568	A -> DEL	LOC_Os04g15590.1	N	frameshift_variant	Average:50.812; most accessible tissue: Callus, score: 79.164	N	N	N	N
vg0408482568	A -> G	LOC_Os04g15590.1	missense_variant&splice_region_variant ; p.Trp22Arg; MODERATE	nonsynonymous_codon ; W22R	Average:50.812; most accessible tissue: Callus, score: 79.164	unknown	unknown	TOLERATED	0.05

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0408482568	NA	3.71E-06	mr1062	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
vg0408482568	NA	4.19E-06	mr1386	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
vg0408482568	NA	4.43E-08	mr1403	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
vg0408482568	NA	1.06E-06	mr1414	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
vg0408482568	NA	4.32E-06	mr1818	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
vg0408482568	NA	3.77E-09	mr1830	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
vg0408482568	1.78E-07	4.69E-20	mr1846	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
vg0408482568	6.61E-07	2.81E-14	mr1846	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
vg0408482568	NA	1.31E-06	mr1304_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
vg0408482568	NA	3.01E-07	mr1608_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
vg0408482568	NA	2.68E-07	mr1608_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
vg0408482568	NA	7.42E-17	mr1830_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
vg0408482568	1.49E-06	1.77E-15	mr1830_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
vg0408482568	4.54E-10	8.54E-36	mr1846_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
vg0408482568	3.09E-13	3.12E-33	mr1846_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