Search for Variation information by Variation ID:

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

Detailed information for vg0232030438:

Variant ID: vg0232030438 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 32030438
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:

CAGTCTTCATTCGCCAAAGACCGCACCACACCCACCGGCAGCTCCTCCTCACACCTAGGTCGCCTCCTCCACCGCCGGCCGCGCCACTCTGCGCCAAGCC[G/A]
GCCTCCTCCACCGGACGCGCCTCGCGCTAATCCGGTCTCCCTCCATCGGTCGCGCCTCCCGCGCCAAGCCGGCCTCTATCTCTGCCGCTCGCGCCTCTCG

Reverse complement sequence

CGAGAGGCGCGAGCGGCAGAGATAGAGGCCGGCTTGGCGCGGGAGGCGCGACCGATGGAGGGAGACCGGATTAGCGCGAGGCGCGTCCGGTGGAGGAGGC[C/T]
GGCTTGGCGCAGAGTGGCGCGGCCGGCGGTGGAGGAGGCGACCTAGGTGTGAGGAGGAGCTGCCGGTGGGTGTGGTGCGGTCTTTGGCGAATGAAGACTG

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	92.10%	2.60%	5.31%	0.00%	NA
All Indica	2759	90.60%	3.90%	5.51%	0.00%	NA
All Japonica	1512	99.90%	0.00%	0.07%	0.00%	NA
Aus	269	63.20%	4.80%	31.97%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	78.10%	8.80%	13.12%	0.00%	NA
Indica III	913	92.10%	3.50%	4.38%	0.00%	NA
Indica Intermediate	786	89.20%	4.30%	6.49%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	2.10%	4.17%	0.00%	NA
Intermediate	90	88.90%	2.20%	8.89%	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
vg0232030438	G -> A	LOC_Os02g52314.1	upstream_gene_variant ; 3286.0bp to feature; MODIFIER	silent_mutation	Average:65.158; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N
vg0232030438	G -> A	LOC_Os02g52330.1	intron_variant ; MODIFIER	silent_mutation	Average:65.158; most accessible tissue: Zhenshan97 panicle, score: 84.824	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0232030438	NA	9.14E-06	mr1336_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
vg0232030438	NA	8.38E-07	mr1712_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
vg0232030438	NA	1.21E-06	mr1717_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
vg0232030438	NA	1.96E-06	mr1722_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
vg0232030438	NA	1.21E-06	mr1910_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
vg0232030438	1.69E-06	3.85E-08	mr1910_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
vg0232030438	NA	2.93E-07	mr1946_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
vg0232030438	NA	2.93E-07	mr1948_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