Search for Variation information by Variation ID:

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

Detailed information for vg0111846225:

Variant ID: vg0111846225 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 11846225
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.26, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CATGAAAAAAATCGTAGCATCAATGTTAAAATTATTGCAATAGATACATATTGCCACAATCTTAAAATCGTTGCTAGCCGTGGTAATAGGTTATTGCAAC[G/A]
ATTTTTATTTAGTTGTAATAAATTTTGTTATTGCCATAAAATGTATGTGGCAAAAAATATATATTGCAACACTTCACATCGTTGCAATAAATAACTATTG

Reverse complement sequence

CAATAGTTATTTATTGCAACGATGTGAAGTGTTGCAATATATATTTTTTGCCACATACATTTTATGGCAATAACAAAATTTATTACAACTAAATAAAAAT[C/T]
GTTGCAATAACCTATTACCACGGCTAGCAACGATTTTAAGATTGTGGCAATATGTATCTATTGCAATAATTTTAACATTGATGCTACGATTTTTTTCATG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.00%	35.20%	0.28%	0.59%	NA
All Indica	2759	95.70%	2.90%	0.40%	1.01%	NA
All Japonica	1512	3.40%	96.60%	0.00%	0.00%	NA
Aus	269	76.20%	23.80%	0.00%	0.00%	NA
Indica I	595	97.50%	0.70%	1.01%	0.84%	NA
Indica II	465	94.40%	4.10%	0.22%	1.29%	NA
Indica III	913	96.50%	2.10%	0.11%	1.31%	NA
Indica Intermediate	786	94.30%	4.70%	0.38%	0.64%	NA
Temperate Japonica	767	2.20%	97.80%	0.00%	0.00%	NA
Tropical Japonica	504	5.40%	94.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	78.10%	21.90%	0.00%	0.00%	NA
Intermediate	90	56.70%	41.10%	2.22%	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
vg0111846225	G -> A	LOC_Os01g21220.1	upstream_gene_variant ; 2991.0bp to feature; MODIFIER	silent_mutation	Average:43.639; most accessible tissue: Callus, score: 59.784	N	N	N	N
vg0111846225	G -> A	LOC_Os01g21220-LOC_Os01g21240	intergenic_region ; MODIFIER	silent_mutation	Average:43.639; most accessible tissue: Callus, score: 59.784	N	N	N	N
vg0111846225	G -> DEL	N	N	silent_mutation	Average:43.639; most accessible tissue: Callus, score: 59.784	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0111846225	5.08E-06	3.69E-14	mr1454_2	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