Search for Variation information by Variation ID:

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

Detailed information for vg0804660474:

Variant ID: vg0804660474 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 4660474
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: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:

TTTCGCATGCGGCCGTCTTAAGTGACCGCATGCGAAGATCGATCTTCGCATGCGGCTGCGACGGCCGCATGCGCAAATGGTAATCTTCGCAGACCATTTC[G/A]
CGCATGCGGGCCGGCCAACCGCATGTGAAGATCGATTCCGCCCGTATGCAAAAACGCTTTCTGTAGTAGTGGTATGTACGATTACTTAAGAAACTAGTAA

Reverse complement sequence

TTACTAGTTTCTTAAGTAATCGTACATACCACTACTACAGAAAGCGTTTTTGCATACGGGCGGAATCGATCTTCACATGCGGTTGGCCGGCCCGCATGCG[C/T]
GAAATGGTCTGCGAAGATTACCATTTGCGCATGCGGCCGTCGCAGCCGCATGCGAAGATCGATCTTCGCATGCGGTCACTTAAGACGGCCGCATGCGAAA

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	62.40%	32.70%	4.95%	0.00%	NA
All Indica	2759	89.50%	2.60%	7.90%	0.00%	NA
All Japonica	1512	4.60%	94.80%	0.53%	0.00%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	81.00%	5.50%	13.45%	0.00%	NA
Indica II	465	81.10%	4.10%	14.84%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	88.80%	2.40%	8.78%	0.00%	NA
Temperate Japonica	767	1.30%	97.90%	0.78%	0.00%	NA
Tropical Japonica	504	11.10%	88.70%	0.20%	0.00%	NA
Japonica Intermediate	241	1.70%	97.90%	0.41%	0.00%	NA
VI/Aromatic	96	93.80%	5.20%	1.04%	0.00%	NA
Intermediate	90	63.30%	28.90%	7.78%	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
vg0804660474	G -> A	LOC_Os08g08180.1	downstream_gene_variant ; 459.0bp to feature; MODIFIER	silent_mutation	Average:29.662; most accessible tissue: Callus, score: 55.279	N	N	N	N
vg0804660474	G -> A	LOC_Os08g08180-LOC_Os08g08190	intergenic_region ; MODIFIER	silent_mutation	Average:29.662; most accessible tissue: Callus, score: 55.279	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0804660474	NA	1.95E-13	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
vg0804660474	NA	2.78E-07	mr1162	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
vg0804660474	NA	3.89E-32	mr1448	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
vg0804660474	NA	2.47E-23	mr1548	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
vg0804660474	NA	4.49E-24	mr1588	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
vg0804660474	NA	4.51E-07	mr1761	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
vg0804660474	NA	2.52E-07	mr1804	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
vg0804660474	1.19E-06	NA	mr1865	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
vg0804660474	NA	2.47E-07	mr1915	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
vg0804660474	NA	1.18E-27	mr1588_2	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
vg0804660474	NA	2.09E-06	mr1588_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
vg0804660474	NA	8.53E-10	mr1761_2	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