Search for Variation information by Variation ID:

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

Detailed information for vg0611626951:

Variant ID: vg0611626951 (JBrowse)	Variation Type: INDEL
Chromosome: chr06	Position: 11626951
Reference Allele: T	Alternative Allele: TA,C
Primary Allele: T	Secondary Allele: TA

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

ATTATCTCTGGTGCAGCAGAAACCCGTCATGCTAACAAAATTTTGGCGTCGCAAACTATTGGAAAAGAGAAGATTGTGGTTCTGAAAGTGTCAATCTGTG[T/TA,C]
ATATCATAGCTTTTGTGGTTGAATGTATATTACTTGTAATTGCAATTGTAAAGTCTCGTTTAAAAAAAAACATACCGGTTTATTCTTCCGTTGCCTTGTG

Reverse complement sequence

CACAAGGCAACGGAAGAATAAACCGGTATGTTTTTTTTTAAACGAGACTTTACAATTGCAATTACAAGTAATATACATTCAACCACAAAAGCTATGATAT[A/TA,G]
CACAGATTGACACTTTCAGAACCACAATCTTCTCTTTTCCAATAGTTTGCGACGCCAAAATTTTGTTAGCATGACGGGTTTCTGCTGCACCAGAGATAAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of TA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	3.60%	0.78%	2.50%	NA
All Indica	2759	89.00%	5.60%	1.27%	4.17%	NA
All Japonica	1512	99.60%	0.20%	0.07%	0.13%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	84.70%	8.60%	3.53%	3.19%	NA
Indica II	465	85.40%	8.20%	1.08%	5.38%	NA
Indica III	913	94.70%	0.50%	0.11%	4.60%	NA
Indica Intermediate	786	87.70%	7.60%	1.02%	3.69%	NA
Temperate Japonica	767	99.30%	0.40%	0.13%	0.13%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	90.60%	9.40%	0.00%	0.00%	NA
Intermediate	90	92.20%	6.70%	1.11%	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
vg0611626951	T -> C	LOC_Os06g20270.1	downstream_gene_variant ; 3110.0bp to feature; MODIFIER	N	Average:46.229; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0611626951	T -> C	LOC_Os06g20260.1	intron_variant ; MODIFIER	N	Average:46.229; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0611626951	T -> DEL	N	N	silent_mutation	Average:46.229; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0611626951	T -> TA	LOC_Os06g20270.1	downstream_gene_variant ; 3109.0bp to feature; MODIFIER	silent_mutation	Average:46.229; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N
vg0611626951	T -> TA	LOC_Os06g20260.1	intron_variant ; MODIFIER	silent_mutation	Average:46.229; most accessible tissue: Minghui63 flag leaf, score: 71.116	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611626951	3.76E-06	NA	mr1528	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