Search for Variation information by Variation ID:

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

Detailed information for vg0211784188:

Variant ID: vg0211784188 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 11784188
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.86, C: 0.15, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:

TCACAAATTTTGAATCAAAATGGTTAGATAGTTTATCTGCATGATCAAAAGGCAAATCTGTTCTATCAGAGTTTCAAGAATAGGATGGGTATCTCTTGCT[T/C]
CCCAACAATGGATTTTAACTTGAATGAGCTTTTTGTTCCTAGAACAGATTTGGAGTGCTTGATTGACATGTTTTGCACACAATAGATTGATAGTCTCATC

Reverse complement sequence

GATGAGACTATCAATCTATTGTGTGCAAAACATGTCAATCAAGCACTCCAAATCTGTTCTAGGAACAAAAAGCTCATTCAAGTTAAAATCCATTGTTGGG[A/G]
AGCAAGAGATACCCATCCTATTCTTGAAACTCTGATAGAACAGATTTGCCTTTTGATCATGCAGATAAACTATCTAACCATTTTGATTCAAAATTTGTGA

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	34.40%	23.60%	2.84%	39.15%	NA
All Indica	2759	2.90%	31.00%	3.99%	62.09%	NA
All Japonica	1512	93.50%	0.20%	1.12%	5.16%	NA
Aus	269	2.20%	92.20%	0.37%	5.20%	NA
Indica I	595	3.20%	21.70%	5.88%	69.24%	NA
Indica II	465	4.10%	35.90%	3.01%	56.99%	NA
Indica III	913	1.90%	32.30%	2.08%	63.75%	NA
Indica Intermediate	786	3.20%	33.70%	5.34%	57.76%	NA
Temperate Japonica	767	93.10%	0.10%	1.04%	5.74%	NA
Tropical Japonica	504	95.60%	0.20%	0.79%	3.37%	NA
Japonica Intermediate	241	90.50%	0.40%	2.07%	7.05%	NA
VI/Aromatic	96	84.40%	1.00%	5.21%	9.38%	NA
Intermediate	90	50.00%	8.90%	1.11%	40.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0211784188	T -> DEL	N	N	silent_mutation	Average:11.85; most accessible tissue: Callus, score: 30.763	N	N	N	N
vg0211784188	T -> C	LOC_Os02g20010.1	intron_variant ; MODIFIER	silent_mutation	Average:11.85; most accessible tissue: Callus, score: 30.763	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0211784188	2.72E-06	7.56E-07	mr1538	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
vg0211784188	NA	7.87E-06	mr1547	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
vg0211784188	NA	2.70E-08	mr1709_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