Search for Variation information by Variation ID:

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

Detailed information for vg0907093222:

Variant ID: vg0907093222 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7093222
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.59, G: 0.42, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTATGTTTGTAAAATTATAATTATTTTAAATTTATTATCAGTAATATAATTATGTTCTCACATATACATGGAAAAAGGTGGGAAGGAGAGAGAAGCGG[T/G]
TGTATTTTTTAAATTGATGTATATAATTTGTGTTTTTATGTTTTTTCTGTAATCTACTTTTATTATAGTACGTTATGTATGTACTTGGTATTTTGGGCTT

Reverse complement sequence

AAGCCCAAAATACCAAGTACATACATAACGTACTATAATAAAAGTAGATTACAGAAAAAACATAAAAACACAAATTATATACATCAATTTAAAAAATACA[A/C]
CCGCTTCTCTCTCCTTCCCACCTTTTTCCATGTATATGTGAGAACATAATTATATTACTGATAATAAATTTAAAATAATTATAATTTTACAAACATAGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.60%	30.80%	0.06%	10.56%	NA
All Indica	2759	87.20%	1.20%	0.04%	11.49%	NA
All Japonica	1512	1.70%	86.70%	0.13%	11.44%	NA
Aus	269	98.10%	0.70%	0.00%	1.12%	NA
Indica I	595	97.00%	0.70%	0.17%	2.18%	NA
Indica II	465	96.10%	0.90%	0.00%	3.01%	NA
Indica III	913	71.30%	0.80%	0.00%	27.93%	NA
Indica Intermediate	786	93.10%	2.40%	0.00%	4.45%	NA
Temperate Japonica	767	1.00%	96.60%	0.26%	2.09%	NA
Tropical Japonica	504	2.00%	83.50%	0.00%	14.48%	NA
Japonica Intermediate	241	3.30%	61.80%	0.00%	34.85%	NA
VI/Aromatic	96	34.40%	65.60%	0.00%	0.00%	NA
Intermediate	90	42.20%	51.10%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907093222	T -> G	LOC_Os09g12410.1	upstream_gene_variant ; 2429.0bp to feature; MODIFIER	silent_mutation	Average:26.64; most accessible tissue: Callus, score: 46.827	N	N	N	N
vg0907093222	T -> G	LOC_Os09g12400.1	downstream_gene_variant ; 836.0bp to feature; MODIFIER	silent_mutation	Average:26.64; most accessible tissue: Callus, score: 46.827	N	N	N	N
vg0907093222	T -> G	LOC_Os09g12390-LOC_Os09g12400	intergenic_region ; MODIFIER	silent_mutation	Average:26.64; most accessible tissue: Callus, score: 46.827	N	N	N	N
vg0907093222	T -> DEL	N	N	silent_mutation	Average:26.64; most accessible tissue: Callus, score: 46.827	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907093222	NA	8.01E-26	mr1024	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
vg0907093222	NA	5.50E-10	mr1128	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
vg0907093222	NA	2.59E-36	mr1542	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
vg0907093222	5.97E-07	4.03E-07	mr1693	Jap_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
vg0907093222	NA	2.98E-08	mr1299_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
vg0907093222	NA	3.52E-14	mr1333_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
vg0907093222	NA	1.53E-11	mr1537_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
vg0907093222	NA	1.07E-08	mr1600_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
vg0907093222	NA	3.65E-08	mr1700_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
vg0907093222	NA	2.02E-07	mr1727_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
vg0907093222	NA	1.13E-07	mr1783_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
vg0907093222	NA	9.87E-08	mr1804_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
vg0907093222	NA	2.41E-35	mr1888_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