Search for Variation information by Variation ID:

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

Detailed information for vg1118396844:

Variant ID: vg1118396844 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18396844
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CCCAATACCTGAATAAAGAGCAATATCATGTTACAACTTTAAATCATTCACACTAGCTACGAATCATTAACAAAGTATAATAATGTATTTGATCAATATC[T/G]
TCTAGTACCACTGCTAAGTTGCATGTTAAAAGAGTAACTTTGCTTGTGTACATCCTGGATGCAGAAACTGGGGATATAATTCATCTCCTTTATCTAAACA

Reverse complement sequence

TGTTTAGATAAAGGAGATGAATTATATCCCCAGTTTCTGCATCCAGGATGTACACAAGCAAAGTTACTCTTTTAACATGCAACTTAGCAGTGGTACTAGA[A/C]
GATATTGATCAAATACATTATTATACTTTGTTAATGATTCGTAGCTAGTGTGAATGATTTAAAGTTGTAACATGATATTGCTCTTTATTCAGGTATTGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.40%	2.30%	3.72%	17.56%	NA
All Indica	2759	63.60%	3.50%	5.47%	27.44%	NA
All Japonica	1512	98.30%	0.10%	0.13%	1.52%	NA
Aus	269	97.80%	0.40%	1.12%	0.74%	NA
Indica I	595	87.60%	0.50%	5.38%	6.55%	NA
Indica II	465	57.20%	3.40%	9.03%	30.32%	NA
Indica III	913	51.00%	5.90%	4.05%	38.99%	NA
Indica Intermediate	786	63.90%	2.90%	5.09%	28.12%	NA
Temperate Japonica	767	99.20%	0.00%	0.00%	0.78%	NA
Tropical Japonica	504	98.20%	0.00%	0.20%	1.59%	NA
Japonica Intermediate	241	95.40%	0.40%	0.41%	3.73%	NA
VI/Aromatic	96	40.60%	7.30%	14.58%	37.50%	NA
Intermediate	90	76.70%	3.30%	6.67%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1118396844	T -> DEL	N	N	silent_mutation	Average:37.313; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg1118396844	T -> G	LOC_Os11g31490.1	downstream_gene_variant ; 3558.0bp to feature; MODIFIER	silent_mutation	Average:37.313; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N
vg1118396844	T -> G	LOC_Os11g31480.1	intron_variant ; MODIFIER	silent_mutation	Average:37.313; most accessible tissue: Zhenshan97 young leaf, score: 53.314	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118396844	3.04E-06	NA	mr1707	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