Search for Variation information by Variation ID:

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

Detailed information for vg0410128864:

Variant ID: vg0410128864 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 10128864
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACCCTGAAATTAAAATTATACAAAAACGGAATGTACTCATCCCAAAGGTAAAATGGAATGTACTCGTTCCAAAGGTTCCGTTTTTGCCAACGGATCACCA[A/G]
TCCGACACTTGAAAAATTTTCACCAAGCTATGTGGGAAGACACGGTATGGATCTAAACCGAGAGAAAAAAAGAGGGAGGGAGTCGGACTCGCCTCCTCTC

Reverse complement sequence

GAGAGGAGGCGAGTCCGACTCCCTCCCTCTTTTTTTCTCTCGGTTTAGATCCATACCGTGTCTTCCCACATAGCTTGGTGAAAATTTTTCAAGTGTCGGA[T/C]
TGGTGATCCGTTGGCAAAAACGGAACCTTTGGAACGAGTACATTCCATTTTACCTTTGGGATGAGTACATTCCGTTTTTGTATAATTTTAATTTCAGGGT

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	35.40%	2.10%	5.67%	56.79%	NA
All Indica	2759	8.40%	0.00%	5.44%	86.08%	NA
All Japonica	1512	85.80%	6.30%	7.08%	0.86%	NA
Aus	269	4.50%	0.00%	2.23%	93.31%	NA
Indica I	595	4.90%	0.00%	8.07%	87.06%	NA
Indica II	465	6.00%	0.00%	4.09%	89.89%	NA
Indica III	913	12.70%	0.00%	5.48%	81.82%	NA
Indica Intermediate	786	7.60%	0.10%	4.20%	88.04%	NA
Temperate Japonica	767	76.70%	11.00%	12.13%	0.26%	NA
Tropical Japonica	504	97.20%	1.60%	0.00%	1.19%	NA
Japonica Intermediate	241	90.90%	1.20%	5.81%	2.07%	NA
VI/Aromatic	96	88.50%	0.00%	0.00%	11.46%	NA
Intermediate	90	53.30%	3.30%	5.56%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0410128864	A -> DEL	N	N	silent_mutation	Average:9.623; most accessible tissue: Callus, score: 31.455	N	N	N	N
vg0410128864	A -> G	LOC_Os04g18350.1	upstream_gene_variant ; 2265.0bp to feature; MODIFIER	silent_mutation	Average:9.623; most accessible tissue: Callus, score: 31.455	N	N	N	N
vg0410128864	A -> G	LOC_Os04g18360.1	downstream_gene_variant ; 3415.0bp to feature; MODIFIER	silent_mutation	Average:9.623; most accessible tissue: Callus, score: 31.455	N	N	N	N
vg0410128864	A -> G	LOC_Os04g18340.1	intron_variant ; MODIFIER	silent_mutation	Average:9.623; most accessible tissue: Callus, score: 31.455	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0410128864	1.67E-06	NA	mr1035	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
vg0410128864	NA	5.88E-07	mr1035	Jap_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
vg0410128864	3.19E-09	NA	mr1062	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
vg0410128864	2.36E-06	1.73E-11	mr1062	Jap_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
vg0410128864	9.01E-09	2.20E-10	mr1525	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
vg0410128864	1.85E-08	1.85E-08	mr1525	Jap_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
vg0410128864	7.46E-06	NA	mr1626	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
vg0410128864	NA	4.14E-06	mr1626	Jap_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
vg0410128864	3.18E-06	NA	mr1035_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
vg0410128864	4.76E-09	NA	mr1062_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
vg0410128864	5.95E-07	1.99E-10	mr1062_2	Jap_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
vg0410128864	3.55E-08	3.54E-08	mr1525_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
vg0410128864	4.04E-06	4.04E-06	mr1525_2	Jap_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
vg0410128864	5.06E-07	NA	mr1631_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
vg0410128864	NA	4.02E-07	mr1631_2	Jap_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