Search for Variation information by Variation ID:

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

Detailed information for vg1110538390:

Variant ID: vg1110538390 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10538390
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: 105. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTGTGGATGACTTTGGCTCACAAACAACGGCAAGCCAGAGCCGTCGTCCTCCACCATGACGAGCAGGTCGGCGAGCTAAGGTGAGAACGGCAGCCGGA[G/A]
CCCCAGCTGCCCAAGGATTCCGACGACGCTGTCGGCGAAGGACACCTTGAACTTGGGCACCATGAACTCGCCGACCCACACCGATTCGGACGCGACGCCA

Reverse complement sequence

TGGCGTCGCGTCCGAATCGGTGTGGGTCGGCGAGTTCATGGTGCCCAAGTTCAAGGTGTCCTTCGCCGACAGCGTCGTCGGAATCCTTGGGCAGCTGGGG[C/T]
TCCGGCTGCCGTTCTCACCTTAGCTCGCCGACCTGCTCGTCATGGTGGAGGACGACGGCTCTGGCTTGCCGTTGTTTGTGAGCCAAAGTCATCCACAAGG

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	86.00%	12.80%	0.04%	1.12%	NA
All Indica	2759	78.40%	21.30%	0.00%	0.29%	NA
All Japonica	1512	99.50%	0.20%	0.07%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	70.10%	29.90%	0.00%	0.00%	NA
Indica III	913	71.50%	27.70%	0.00%	0.77%	NA
Indica Intermediate	786	77.50%	22.40%	0.00%	0.13%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.20%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	54.20%	3.10%	1.04%	41.67%	NA
Intermediate	90	85.60%	12.20%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110538390	G -> A	LOC_Os11g18660.1	missense_variant ; p.Leu102Phe; MODERATE	nonsynonymous_codon ; L102F	Average:62.976; most accessible tissue: Zhenshan97 young leaf, score: 84.035	possibly damaging	1.952	DELETERIOUS	0.00
vg1110538390	G -> DEL	LOC_Os11g18660.1	N	frameshift_variant	Average:62.976; most accessible tissue: Zhenshan97 young leaf, score: 84.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110538390	NA	8.31E-06	mr1580	Ind_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
vg1110538390	NA	5.49E-06	mr1956	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
vg1110538390	NA	7.73E-06	mr1956	Ind_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
vg1110538390	NA	9.28E-06	mr1958	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
vg1110538390	NA	3.08E-09	mr1322_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
vg1110538390	NA	1.89E-12	mr1325_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
vg1110538390	NA	2.18E-06	mr1325_2	Ind_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
vg1110538390	6.97E-07	1.46E-09	mr1335_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