Search for Variation information by Variation ID:

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

Detailed information for vg1222302867:

Variant ID: vg1222302867 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22302867
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.01, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

AACATGCTATAGAGCAGGTACAATAGCAGGCTATAAGCCAGCTGCAAACATATTTTAAGAAGATAAATTAGGAGAGAGAAGAGCAGTGGGCTACAGATTT[G/A]
TAGCCAGCTGTAGCACGGACTCCAAGACGCAGTGTGTCTATGACAGGTGGGACTAGATATTAATAGTGTAGTATGTAACTATTGTATGAATGAACTACTA

Reverse complement sequence

TAGTAGTTCATTCATACAATAGTTACATACTACACTATTAATATCTAGTCCCACCTGTCATAGACACACTGCGTCTTGGAGTCCGTGCTACAGCTGGCTA[C/T]
AAATCTGTAGCCCACTGCTCTTCTCTCTCCTAATTTATCTTCTTAAAATATGTTTGCAGCTGGCTTATAGCCTGCTATTGTACCTGCTCTATAGCATGTT

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	40.30%	39.80%	0.49%	19.42%	NA
All Indica	2759	61.80%	14.60%	0.51%	23.12%	NA
All Japonica	1512	9.10%	84.70%	0.26%	5.89%	NA
Aus	269	17.10%	15.20%	1.49%	66.17%	NA
Indica I	595	75.60%	11.40%	0.17%	12.77%	NA
Indica II	465	61.70%	22.40%	1.29%	14.62%	NA
Indica III	913	57.00%	10.50%	0.33%	32.20%	NA
Indica Intermediate	786	57.00%	17.00%	0.51%	25.45%	NA
Temperate Japonica	767	3.10%	88.50%	0.39%	7.95%	NA
Tropical Japonica	504	20.80%	79.00%	0.00%	0.20%	NA
Japonica Intermediate	241	3.70%	84.60%	0.41%	11.20%	NA
VI/Aromatic	96	2.10%	93.80%	0.00%	4.17%	NA
Intermediate	90	16.70%	72.20%	1.11%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222302867	G -> DEL	N	N	silent_mutation	Average:57.006; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg1222302867	G -> A	LOC_Os12g36440.1	upstream_gene_variant ; 982.0bp to feature; MODIFIER	silent_mutation	Average:57.006; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg1222302867	G -> A	LOC_Os12g36450.1	upstream_gene_variant ; 2231.0bp to feature; MODIFIER	silent_mutation	Average:57.006; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg1222302867	G -> A	LOC_Os12g36440-LOC_Os12g36450	intergenic_region ; MODIFIER	silent_mutation	Average:57.006; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222302867	2.71E-06	2.04E-06	mr1626	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