Search for Variation information by Variation ID:

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

Detailed information for vg1105181691:

Variant ID: vg1105181691 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5181691
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:

GACCTACTATCCCGATCGCCAGTGCACGTCAGCGAACGGAACGGAGTAGACTACGTGCGATGACATAGTACAGAGAAGGAGGTAAATTCTAGATTGCTTT[G/T]
CACGTGTGTTACGAGGTGGCAGCGGCTCGGTTTATATAGAGATATCAGGACACGTGATTAGGACGCCTTCATAATCTCCGCACTACATAACCGAACCGGA

Reverse complement sequence

TCCGGTTCGGTTATGTAGTGCGGAGATTATGAAGGCGTCCTAATCACGTGTCCTGATATCTCTATATAAACCGAGCCGCTGCCACCTCGTAACACACGTG[C/A]
AAAGCAATCTAGAATTTACCTCCTTCTCTGTACTATGTCATCGCACGTAGTCTACTCCGTTCCGTTCGCTGACGTGCACTGGCGATCGGGATAGTAGGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.20%	9.70%	0.38%	33.71%	NA
All Indica	2759	46.50%	0.70%	0.62%	52.23%	NA
All Japonica	1512	70.90%	27.70%	0.00%	1.39%	NA
Aus	269	63.20%	0.70%	0.00%	36.06%	NA
Indica I	595	22.40%	2.00%	0.84%	74.79%	NA
Indica II	465	19.40%	0.20%	1.08%	79.35%	NA
Indica III	913	67.80%	0.10%	0.22%	31.87%	NA
Indica Intermediate	786	56.00%	0.60%	0.64%	42.75%	NA
Temperate Japonica	767	64.50%	33.10%	0.00%	2.35%	NA
Tropical Japonica	504	85.70%	14.10%	0.00%	0.20%	NA
Japonica Intermediate	241	60.20%	39.00%	0.00%	0.83%	NA
VI/Aromatic	96	84.40%	5.20%	1.04%	9.38%	NA
Intermediate	90	55.60%	16.70%	0.00%	27.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105181691	G -> T	LOC_Os11g09710.1	upstream_gene_variant ; 721.0bp to feature; MODIFIER	silent_mutation	Average:13.357; most accessible tissue: Callus, score: 79.274	N	N	N	N
vg1105181691	G -> T	LOC_Os11g09720.1	upstream_gene_variant ; 3031.0bp to feature; MODIFIER	silent_mutation	Average:13.357; most accessible tissue: Callus, score: 79.274	N	N	N	N
vg1105181691	G -> T	LOC_Os11g09700.1	downstream_gene_variant ; 2681.0bp to feature; MODIFIER	silent_mutation	Average:13.357; most accessible tissue: Callus, score: 79.274	N	N	N	N
vg1105181691	G -> T	LOC_Os11g09700-LOC_Os11g09710	intergenic_region ; MODIFIER	silent_mutation	Average:13.357; most accessible tissue: Callus, score: 79.274	N	N	N	N
vg1105181691	G -> DEL	N	N	silent_mutation	Average:13.357; most accessible tissue: Callus, score: 79.274	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105181691	1.94E-06	1.94E-06	mr1957_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