Search for Variation information by Variation ID:

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

Detailed information for vg0820435145:

Variant ID: vg0820435145 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20435145
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

CTCCGTTTCATAATGTAAGTCATTCTAGCATTTTCCACATTAATAATAATGTTAATGAATCTAAATAGATATATATGTCTAGATTCATTAATATCAATAT[G/A]
AATGTGGAAAATGCTAGAATGACTTATATTGTGAAACGGAGGGAGTACTAGTATACACAAATGTATTTATTTGACATGCATAAAAATCTAATTAATTGAC

Reverse complement sequence

GTCAATTAATTAGATTTTTATGCATGTCAAATAAATACATTTGTGTATACTAGTACTCCCTCCGTTTCACAATATAAGTCATTCTAGCATTTTCCACATT[C/T]
ATATTGATATTAATGAATCTAGACATATATATCTATTTAGATTCATTAACATTATTATTAATGTGGAAAATGCTAGAATGACTTACATTATGAAACGGAG

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	84.40%	6.10%	3.45%	5.99%	NA
All Indica	2759	81.00%	4.00%	5.07%	9.93%	NA
All Japonica	1512	93.00%	5.60%	1.32%	0.07%	NA
Aus	269	87.00%	11.50%	0.37%	1.12%	NA
Indica I	595	98.30%	0.30%	0.17%	1.18%	NA
Indica II	465	93.50%	3.00%	1.51%	1.94%	NA
Indica III	913	65.50%	5.90%	11.94%	16.65%	NA
Indica Intermediate	786	78.40%	5.20%	2.93%	13.49%	NA
Temperate Japonica	767	96.60%	1.60%	1.83%	0.00%	NA
Tropical Japonica	504	87.90%	11.30%	0.60%	0.20%	NA
Japonica Intermediate	241	92.10%	6.60%	1.24%	0.00%	NA
VI/Aromatic	96	45.80%	53.10%	1.04%	0.00%	NA
Intermediate	90	80.00%	13.30%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0820435145	G -> A	LOC_Os08g32940.1	upstream_gene_variant ; 4108.0bp to feature; MODIFIER	silent_mutation	Average:50.19; most accessible tissue: Minghui63 root, score: 74.461	N	N	N	N
vg0820435145	G -> A	LOC_Os08g32940-LOC_Os08g32950	intergenic_region ; MODIFIER	silent_mutation	Average:50.19; most accessible tissue: Minghui63 root, score: 74.461	N	N	N	N
vg0820435145	G -> DEL	N	N	silent_mutation	Average:50.19; most accessible tissue: Minghui63 root, score: 74.461	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820435145	NA	7.57E-06	mr1227	Jap_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
vg0820435145	6.87E-06	6.87E-06	mr1439_2	Jap_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