Search for Variation information by Variation ID:

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

Detailed information for vg1110000666:

Variant ID: vg1110000666 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10000666
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.66, A: 0.36, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCAAAAGCCATGTAACCATCTTGCAAAGATTAGTACAGATCTTGATCACAGAGAATATCATCATCACAACTTGGTGGTGTCACAAGCTGGGTAAAATC[A/G]
CTAATGATATCGTATTGTTGAAGCACACGTCAGGCCTAGCGGCCGGCCGCCTCCACGCGCCTCCGCCCGTGGTGGCACGACAGGGCCCCAGCCTCGACCT

Reverse complement sequence

AGGTCGAGGCTGGGGCCCTGTCGTGCCACCACGGGCGGAGGCGCGTGGAGGCGGCCGGCCGCTAGGCCTGACGTGTGCTTCAACAATACGATATCATTAG[T/C]
GATTTTACCCAGCTTGTGACACCACCAAGTTGTGATGATGATATTCTCTGTGATCAAGATCTGTACTAATCTTTGCAAGATGGTTACATGGCTTTTGGAC

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	43.80%	7.80%	0.23%	48.16%	NA
All Indica	2759	20.10%	7.70%	0.25%	71.95%	NA
All Japonica	1512	93.70%	4.00%	0.00%	2.38%	NA
Aus	269	16.00%	5.90%	1.49%	76.58%	NA
Indica I	595	38.80%	5.50%	0.17%	55.46%	NA
Indica II	465	12.70%	3.90%	0.22%	83.23%	NA
Indica III	913	5.70%	12.40%	0.11%	81.82%	NA
Indica Intermediate	786	27.00%	6.20%	0.51%	66.28%	NA
Temperate Japonica	767	93.00%	4.40%	0.00%	2.61%	NA
Tropical Japonica	504	94.00%	3.20%	0.00%	2.78%	NA
Japonica Intermediate	241	95.00%	4.10%	0.00%	0.83%	NA
VI/Aromatic	96	18.80%	70.80%	0.00%	10.42%	NA
Intermediate	90	44.40%	12.20%	0.00%	43.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110000666	A -> DEL	N	N	silent_mutation	Average:10.541; most accessible tissue: Callus, score: 43.751	N	N	N	N
vg1110000666	A -> G	LOC_Os11g17850.1	downstream_gene_variant ; 3460.0bp to feature; MODIFIER	silent_mutation	Average:10.541; most accessible tissue: Callus, score: 43.751	N	N	N	N
vg1110000666	A -> G	LOC_Os11g17850-LOC_Os11g17870	intergenic_region ; MODIFIER	silent_mutation	Average:10.541; most accessible tissue: Callus, score: 43.751	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110000666	4.11E-06	3.82E-06	mr1860	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