Search for Variation information by Variation ID:

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

Detailed information for vg1116376902:

Variant ID: vg1116376902 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 16376902
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, C: 0.23, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTCTGTGATTGATCTATTTTTTTATCGTCTATTTACCTATCGTTTCATAACAAAAAATCACTAAGAACACAGGCAACAAGGGAACACTATCAAACTCT[C/T]
CTTCTCTTATGATGCCTGCAACACTGCAATGCCATCCGGCACTTGCTCTGTATTTCTTCCTAGTGCCTCTCGTTCTTAACGACCTGACTATATGCGTACT

Reverse complement sequence

AGTACGCATATAGTCAGGTCGTTAAGAACGAGAGGCACTAGGAAGAAATACAGAGCAAGTGCCGGATGGCATTGCAGTGTTGCAGGCATCATAAGAGAAG[G/A]
AGAGTTTGATAGTGTTCCCTTGTTGCCTGTGTTCTTAGTGATTTTTTGTTATGAAACGATAGGTAAATAGACGATAAAAAAATAGATCAATCACAGAAAA

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	21.20%	4.70%	0.28%	73.85%	NA
All Indica	2759	2.10%	6.60%	0.40%	90.83%	NA
All Japonica	1512	54.80%	2.10%	0.13%	42.92%	NA
Aus	269	3.00%	0.00%	0.00%	97.03%	NA
Indica I	595	1.30%	8.40%	0.17%	90.08%	NA
Indica II	465	1.30%	3.20%	0.65%	94.84%	NA
Indica III	913	0.90%	5.70%	0.00%	93.43%	NA
Indica Intermediate	786	4.70%	8.40%	0.89%	86.01%	NA
Temperate Japonica	767	84.20%	1.30%	0.00%	14.47%	NA
Tropical Japonica	504	24.80%	3.20%	0.20%	71.83%	NA
Japonica Intermediate	241	24.10%	2.50%	0.41%	73.03%	NA
VI/Aromatic	96	88.50%	4.20%	0.00%	7.29%	NA
Intermediate	90	24.40%	1.10%	0.00%	74.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1116376902	C -> T	LOC_Os11g28460.1	upstream_gene_variant ; 2794.0bp to feature; MODIFIER	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N
vg1116376902	C -> T	LOC_Os11g28430.1	downstream_gene_variant ; 4418.0bp to feature; MODIFIER	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N
vg1116376902	C -> T	LOC_Os11g28440.1	downstream_gene_variant ; 451.0bp to feature; MODIFIER	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N
vg1116376902	C -> T	LOC_Os11g28450.1	downstream_gene_variant ; 989.0bp to feature; MODIFIER	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N
vg1116376902	C -> T	LOC_Os11g28440-LOC_Os11g28450	intergenic_region ; MODIFIER	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N
vg1116376902	C -> DEL	N	N	silent_mutation	Average:12.475; most accessible tissue: Callus, score: 54.237	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1116376902	4.35E-06	NA	mr1265	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