Search for Variation information by Variation ID:

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

Detailed information for vg0706052872:

Variant ID: vg0706052872 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 6052872
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 272. )

Flanking Sequence (100 bp) in Reference Genome:

TTGTCCTTTTCTTTTTCTCTCCAAATCGTGATTTTTCCAAAGGAAAAAAAGTTTTTTTCCTTGTCCCTCAACTCTTGGTTTGGTTTGGTTTGTATTTCTC[G/A]
TCTCCAAAACTGATAAAACTCGTCCGTCAACTCTCAAAACTGTTTAGATCTCACCTCTCACTCGTTTATAAGTGGTTTTTGACCTACTTGGTGTAGATAT

Reverse complement sequence

ATATCTACACCAAGTAGGTCAAAAACCACTTATAAACGAGTGAGAGGTGAGATCTAAACAGTTTTGAGAGTTGACGGACGAGTTTTATCAGTTTTGGAGA[C/T]
GAGAAATACAAACCAAACCAAACCAAGAGTTGAGGGACAAGGAAAAAAACTTTTTTTCCTTTGGAAAAATCACGATTTGGAGAGAAAAAGAAAAGGACAA

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	94.40%	5.60%	0.02%	0.00%	NA
All Indica	2759	97.40%	2.60%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	30.50%	69.50%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	96.50%	3.40%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	5.00%	0.00%	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%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg0706052872	G -> A	LOC_Os07g11010.1	intron_variant ; MODIFIER	silent_mutation	Average:57.806; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg0706052872	G -> A	LOC_Os07g11010.2	intron_variant ; MODIFIER	silent_mutation	Average:57.806; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0706052872	NA	6.99E-43	mr1550	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
vg0706052872	NA	2.40E-06	mr1931	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
vg0706052872	NA	8.77E-20	mr1095_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
vg0706052872	8.53E-06	NA	mr1151_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
vg0706052872	4.63E-06	NA	mr1243_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
vg0706052872	8.50E-06	NA	mr1248_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
vg0706052872	NA	5.03E-43	mr1550_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
vg0706052872	NA	2.57E-29	mr1757_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
vg0706052872	NA	5.19E-07	mr1762_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
vg0706052872	NA	7.63E-10	mr1818_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