Search for Variation information by Variation ID:

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

Detailed information for vg0621039858:

Variant ID: vg0621039858 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 21039858
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: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CATCAATTTGTTTGGTTGATTCCTATTGACTTGAAAAGAATTTGGACGTGGGACTAGAACCATTGGAAATGTTATCTTCTTAGCTTTCCATCCATATAAA[G/A]
AACACCCTAATCCGAGCATGTATGCGATCTGGGCGTCCGTTTTAGTGCAGACTAGTCTTGGACTCCGAATAATACTCGAAGTCGACTTGGTTGAGCCTCC

Reverse complement sequence

GGAGGCTCAACCAAGTCGACTTCGAGTATTATTCGGAGTCCAAGACTAGTCTGCACTAAAACGGACGCCCAGATCGCATACATGCTCGGATTAGGGTGTT[C/T]
TTTATATGGATGGAAAGCTAAGAAGATAACATTTCCAATGGTTCTAGTCCCACGTCCAAATTCTTTTCAAGTCAATAGGAATCAACCAAACAAATTGATG

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	88.30%	11.70%	0.04%	0.00%	NA
All Indica	2759	80.60%	19.30%	0.07%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	97.80%	2.20%	0.00%	0.00%	NA
Indica II	465	85.60%	14.00%	0.43%	0.00%	NA
Indica III	913	60.60%	39.40%	0.00%	0.00%	NA
Indica Intermediate	786	88.00%	12.00%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	92.20%	7.80%	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
vg0621039858	G -> A	LOC_Os06g36000.1	upstream_gene_variant ; 855.0bp to feature; MODIFIER	silent_mutation	Average:47.682; most accessible tissue: Minghui63 root, score: 81.852	N	N	N	N
vg0621039858	G -> A	LOC_Os06g35990-LOC_Os06g36000	intergenic_region ; MODIFIER	silent_mutation	Average:47.682; most accessible tissue: Minghui63 root, score: 81.852	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0621039858	9.37E-07	NA	mr1695_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
vg0621039858	5.53E-06	1.68E-06	mr1695_2	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