Search for Variation information by Variation ID:

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

Detailed information for vg1119011995:

Variant ID: vg1119011995 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19011995
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: 295. )

Flanking Sequence (100 bp) in Reference Genome:

GTCAGCCTTCATCCACTCAGGAAATACCGAGGATGTCTTCTACTTCTACTGGTATATATCGTGTGCCACAATAGAGGCAATAAAGATGCCCAAAAGGGCT[G/A]
TAAAGATCCAAACTTCATCTCCTCATCCTCGGCATTCCACAACCATTGGCACACCAAATTCCCATGTGATAACCATTTACTTAGCCAGAGGCATCTCATA

Reverse complement sequence

TATGAGATGCCTCTGGCTAAGTAAATGGTTATCACATGGGAATTTGGTGTGCCAATGGTTGTGGAATGCCGAGGATGAGGAGATGAAGTTTGGATCTTTA[C/T]
AGCCCTTTTGGGCATCTTTATTGCCTCTATTGTGGCACACGATATATACCAGTAGAAGTAGAAGACATCCTCGGTATTTCCTGAGTGGATGAAGGCTGAC

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	66.50%	1.70%	6.43%	25.37%	NA
All Indica	2759	73.60%	0.80%	5.40%	20.15%	NA
All Japonica	1512	47.20%	2.80%	9.79%	40.28%	NA
Aus	269	99.30%	0.00%	0.00%	0.74%	NA
Indica I	595	90.90%	0.00%	1.68%	7.39%	NA
Indica II	465	65.20%	0.90%	10.11%	23.87%	NA
Indica III	913	65.10%	1.10%	6.13%	27.71%	NA
Indica Intermediate	786	75.60%	1.00%	4.58%	18.83%	NA
Temperate Japonica	767	61.00%	1.00%	3.00%	34.94%	NA
Tropical Japonica	504	30.80%	3.20%	19.44%	46.63%	NA
Japonica Intermediate	241	37.30%	7.50%	11.20%	43.98%	NA
VI/Aromatic	96	61.50%	9.40%	4.17%	25.00%	NA
Intermediate	90	78.90%	8.90%	3.33%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1119011995	G -> A	LOC_Os11g32180.1	upstream_gene_variant ; 3403.0bp to feature; MODIFIER	silent_mutation	Average:59.482; most accessible tissue: Minghui63 young leaf, score: 78.054	N	N	N	N
vg1119011995	G -> A	LOC_Os11g32190.1	downstream_gene_variant ; 3521.0bp to feature; MODIFIER	silent_mutation	Average:59.482; most accessible tissue: Minghui63 young leaf, score: 78.054	N	N	N	N
vg1119011995	G -> A	LOC_Os11g32180-LOC_Os11g32190	intergenic_region ; MODIFIER	silent_mutation	Average:59.482; most accessible tissue: Minghui63 young leaf, score: 78.054	N	N	N	N
vg1119011995	G -> DEL	N	N	silent_mutation	Average:59.482; most accessible tissue: Minghui63 young leaf, score: 78.054	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119011995	6.27E-08	2.62E-09	mr1350_2	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