Search for Variation information by Variation ID:

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

Detailed information for vg0516825897:

Variant ID: vg0516825897 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 16825897
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.15, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

GGCGTACGGTTACGAGGATATCGGCCTGGATCTCGAGAATCCTGTCATCGTCTCCCGCTGTTGTCTCGGCTCCGGTCTCCATCATTGTCGTCGTTATGGC[G/A]
ACGTCCTCGACCGGTATCGTCTGGCACCTGTCGTTCGCGATCGTTGTGATCGTGGTGGTTGTGGCGGTTATCATGGTCTCGGTCCTCGTTTGAGCGGTCT

Reverse complement sequence

AGACCGCTCAAACGAGGACCGAGACCATGATAACCGCCACAACCACCACGATCACAACGATCGCGAACGACAGGTGCCAGACGATACCGGTCGAGGACGT[C/T]
GCCATAACGACGACAATGATGGAGACCGGAGCCGAGACAACAGCGGGAGACGATGACAGGATTCTCGAGATCCAGGCCGATATCCTCGTAACCGTACGCC

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	54.00%	45.40%	0.36%	0.17%	NA
All Indica	2759	82.60%	16.60%	0.58%	0.25%	NA
All Japonica	1512	1.90%	98.10%	0.00%	0.00%	NA
Aus	269	78.80%	21.20%	0.00%	0.00%	NA
Indica I	595	94.10%	5.20%	0.34%	0.34%	NA
Indica II	465	60.90%	38.10%	1.08%	0.00%	NA
Indica III	913	87.80%	11.80%	0.22%	0.11%	NA
Indica Intermediate	786	80.50%	18.10%	0.89%	0.51%	NA
Temperate Japonica	767	2.60%	97.40%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	37.80%	60.00%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0516825897	G -> DEL	N	N	silent_mutation	Average:60.755; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg0516825897	G -> A	LOC_Os05g28690.1	upstream_gene_variant ; 4229.0bp to feature; MODIFIER	silent_mutation	Average:60.755; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N
vg0516825897	G -> A	LOC_Os05g28680.1	intron_variant ; MODIFIER	silent_mutation	Average:60.755; most accessible tissue: Zhenshan97 young leaf, score: 78.044	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0516825897	NA	5.21E-07	mr1343	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
vg0516825897	NA	9.73E-10	mr1399	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
vg0516825897	4.74E-06	4.73E-06	mr1717	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
vg0516825897	NA	2.24E-11	mr1902	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
vg0516825897	NA	1.12E-07	mr1399_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