Search for Variation information by Variation ID:

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

Detailed information for vg1121667268:

Variant ID: vg1121667268 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 21667268
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 66. )

Flanking Sequence (100 bp) in Reference Genome:

TTCCATCCAGGTGACGCACGATGATGCTGGAGACGGTGGCGGCGGTGCCGGCCACCGGGGATGGTGGGCGGCATATGCTGCTCCACCTCTGCTCGCTCCG[C/T]
GACATCAAGCACAGCGACGGCTGGATCCGTGTGTTGTTGGAGGAGGCTGAGAACGAGAGGATGCACCTCATGGCCTTCATGGCGGTGCCCAAGCGGAGGT

Reverse complement sequence

ACCTCCGCTTGGGCACCGCCATGAAGGCCATGAGGTGCATCCTCTCGTTCTCAGCCTCCTCCAACAACACACGGATCCAGCCGTCGCTGTGCTTGATGTC[G/A]
CGGAGCGAGCAGAGGTGGAGCAGCATATGCCGCCCACCATCCCCGGTGGCCGGCACCGCCGCCACCGTCTCCAGCATCATCGTGCGTCACCTGGATGGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	49.90%	14.00%	1.29%	34.81%	NA
All Indica	2759	39.10%	14.80%	1.74%	44.29%	NA
All Japonica	1512	71.40%	10.60%	0.26%	17.66%	NA
Aus	269	54.60%	24.20%	0.74%	20.45%	NA
Indica I	595	22.40%	47.90%	1.01%	28.74%	NA
Indica II	465	41.90%	3.00%	2.37%	52.69%	NA
Indica III	913	44.40%	4.40%	1.64%	49.62%	NA
Indica Intermediate	786	44.10%	8.90%	2.04%	44.91%	NA
Temperate Japonica	767	83.20%	7.80%	0.00%	9.00%	NA
Tropical Japonica	504	56.20%	16.50%	0.60%	26.79%	NA
Japonica Intermediate	241	66.00%	7.50%	0.41%	26.14%	NA
VI/Aromatic	96	8.30%	6.20%	4.17%	81.25%	NA
Intermediate	90	48.90%	22.20%	3.33%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1121667268	C -> T	LOC_Os11g36690.1	downstream_gene_variant ; 102.0bp to feature; MODIFIER	silent_mutation	Average:42.528; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg1121667268	C -> T	LOC_Os11g36690-LOC_Os11g36700	intergenic_region ; MODIFIER	silent_mutation	Average:42.528; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg1121667268	C -> DEL	N	N	silent_mutation	Average:42.528; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1121667268	NA	1.49E-06	mr1014	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
vg1121667268	NA	2.85E-06	mr1479	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
vg1121667268	NA	4.06E-08	mr1662	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
vg1121667268	NA	1.40E-06	mr1662	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
vg1121667268	NA	4.07E-06	mr1835	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
vg1121667268	NA	7.19E-07	mr1662_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