Search for Variation information by Variation ID:

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

Detailed information for vg1123159214:

Variant ID: vg1123159214 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 23159214
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, A: 0.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

GTCGCTGGATGGGGATCATGGATGGGTAGGTAGCTTGCCGAGGGTTTCGTATGCATGGAACGGGGAGGGGTTTTGCGATTGAGCTAATGTAAGGGCAATC[G/A]
TTGCGACTCTTTCGGTGCTTTGTTTGTAGGTTTTTATATTTATGTGTGTTAATGTAGGAGATTGGTTTTGGCCATTAATGTGCTTAGGGGATAAGGCGAC

Reverse complement sequence

GTCGCCTTATCCCCTAAGCACATTAATGGCCAAAACCAATCTCCTACATTAACACACATAAATATAAAAACCTACAAACAAAGCACCGAAAGAGTCGCAA[C/T]
GATTGCCCTTACATTAGCTCAATCGCAAAACCCCTCCCCGTTCCATGCATACGAAACCCTCGGCAAGCTACCTACCCATCCATGATCCCCATCCAGCGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.40%	2.60%	0.00%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.00%	0.00%	NA
All Japonica	1512	98.90%	1.10%	0.00%	0.00%	NA
Aus	269	77.00%	23.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.30%	0.70%	0.00%	0.00%	NA
Indica Intermediate	786	97.30%	2.70%	0.00%	0.00%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	0.00%	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
vg1123159214	G -> A	LOC_Os11g38890.1	downstream_gene_variant ; 4558.0bp to feature; MODIFIER	silent_mutation	Average:77.32; most accessible tissue: Zhenshan97 flower, score: 85.564	N	N	N	N
vg1123159214	G -> A	LOC_Os11g38900.1	intron_variant ; MODIFIER	silent_mutation	Average:77.32; most accessible tissue: Zhenshan97 flower, score: 85.564	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1123159214	4.22E-06	NA	mr1020	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