Search for Variation information by Variation ID:

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

Detailed information for vg0412758955:

Variant ID: vg0412758955 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 12758955
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, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCAGAAGTTTAGAGACATTTGGACACTTATTTTGTGAGATGTGTGGATATTTATAAAGATTATTCAGATTAAGCTATGTCCACACATAGGGGAGCAAT[G/A]
ACCATGTAAAAGCTCCAAAAATAGTCTCTTACTGCATAGTCGATGATGCAGTTAGATTTTAAAGCATGTTATGATTAATCATATATATAAGAATATTTCC

Reverse complement sequence

GGAAATATTCTTATATATATGATTAATCATAACATGCTTTAAAATCTAACTGCATCATCGACTATGCAGTAAGAGACTATTTTTGGAGCTTTTACATGGT[C/T]
ATTGCTCCCCTATGTGTGGACATAGCTTAATCTGAATAATCTTTATAAATATCCACACATCTCACAAAATAAGTGTCCAAATGTCTCTAAACTTCTGAGA

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	36.60%	9.10%	15.07%	39.21%	NA
All Indica	2759	4.00%	11.40%	21.38%	63.28%	NA
All Japonica	1512	98.30%	0.00%	0.40%	1.32%	NA
Aus	269	0.40%	42.80%	36.06%	20.82%	NA
Indica I	595	3.20%	9.90%	12.10%	74.79%	NA
Indica II	465	8.20%	6.50%	15.91%	69.46%	NA
Indica III	913	1.90%	16.00%	31.11%	51.04%	NA
Indica Intermediate	786	4.50%	10.10%	20.36%	65.14%	NA
Temperate Japonica	767	98.60%	0.00%	0.39%	1.04%	NA
Tropical Japonica	504	98.80%	0.00%	0.40%	0.79%	NA
Japonica Intermediate	241	96.30%	0.00%	0.41%	3.32%	NA
VI/Aromatic	96	88.50%	0.00%	4.17%	7.29%	NA
Intermediate	90	54.40%	2.20%	16.67%	26.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0412758955	G -> DEL	N	N	silent_mutation	Average:9.218; most accessible tissue: Callus, score: 32.025	N	N	N	N
vg0412758955	G -> A	LOC_Os04g22520.1	upstream_gene_variant ; 2011.0bp to feature; MODIFIER	silent_mutation	Average:9.218; most accessible tissue: Callus, score: 32.025	N	N	N	N
vg0412758955	G -> A	LOC_Os04g22510-LOC_Os04g22520	intergenic_region ; MODIFIER	silent_mutation	Average:9.218; most accessible tissue: Callus, score: 32.025	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0412758955	NA	1.37E-12	mr1149	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0412758955	NA	4.53E-06	mr1149	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0412758955	NA	3.46E-06	mr1798	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0412758955	1.71E-07	8.47E-07	mr1887	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