Search for Variation information by Variation ID:

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

Detailed information for vg1128831356:

Variant ID: vg1128831356 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 28831356
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.92, C: 0.09, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:

TTCTGGTGCTTGTTGGCTTTGAAGAGAAACACTGAGAATCAACAAAGTATTTTTACTCGTTATAAAAACTGCCATACTGAAAGTATTTTCTCTGTCAGTA[C/T]
GGCAGTTCTCTTAACGAGTGAAAACACACTTTCTGGTGCTTGTTGGCTTTCAAGAGAAACACCAGAAGCTAATAATACGTTTAAGTACCCACATTGGAAG

Reverse complement sequence

CTTCCAATGTGGGTACTTAAACGTATTATTAGCTTCTGGTGTTTCTCTTGAAAGCCAACAAGCACCAGAAAGTGTGTTTTCACTCGTTAAGAGAACTGCC[G/A]
TACTGACAGAGAAAATACTTTCAGTATGGCAGTTTTTATAACGAGTAAAAATACTTTGTTGATTCTCAGTGTTTCTCTTCAAAGCCAACAAGCACCAGAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.70%	34.30%	0.74%	0.19%	NA
All Indica	2759	60.40%	38.90%	0.36%	0.33%	NA
All Japonica	1512	75.90%	23.50%	0.53%	0.00%	NA
Aus	269	39.40%	56.50%	4.09%	0.00%	NA
Indica I	595	43.40%	55.80%	0.84%	0.00%	NA
Indica II	465	38.10%	60.90%	0.00%	1.08%	NA
Indica III	913	85.00%	14.70%	0.11%	0.22%	NA
Indica Intermediate	786	57.90%	41.30%	0.51%	0.25%	NA
Temperate Japonica	767	58.30%	41.50%	0.26%	0.00%	NA
Tropical Japonica	504	95.20%	3.60%	1.19%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	7.30%	3.12%	0.00%	NA
Intermediate	90	60.00%	36.70%	3.33%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1128831356	C -> T	LOC_Os11g47809.1	downstream_gene_variant ; 2843.0bp to feature; MODIFIER	silent_mutation	Average:38.322; most accessible tissue: Callus, score: 60.557	N	N	N	N
vg1128831356	C -> T	LOC_Os11g47809-LOC_Os11g47820	intergenic_region ; MODIFIER	silent_mutation	Average:38.322; most accessible tissue: Callus, score: 60.557	N	N	N	N
vg1128831356	C -> DEL	N	N	silent_mutation	Average:38.322; most accessible tissue: Callus, score: 60.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1128831356	NA	1.32E-06	mr1310	Jap_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
vg1128831356	NA	2.20E-06	mr1644	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
vg1128831356	3.65E-06	3.65E-06	mr1899	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
vg1128831356	NA	4.43E-07	mr1191_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
vg1128831356	NA	5.29E-06	mr1959_2	Jap_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