Search for Variation information by Variation ID:

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

Detailed information for vg0624615989:

Variant ID: vg0624615989 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 24615989
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:

ATAAATTTACAAGTAAAGCAAGTGTGAGAAATAAAATGACATGGTTAAATTTAATTTTTTTAAATTCTCCATGATTAGTTACACTCGTTAAAATTTTATT[G/A]
GAATTTTCAGAGCTTAATTGCTAATTTTAATAATACAAACATCATTTAAAAATTATTTAATTAAAAAAGAAAGAAACTACTTCCTTTTAGGTTTGCTTCG

Reverse complement sequence

CGAAGCAAACCTAAAAGGAAGTAGTTTCTTTCTTTTTTAATTAAATAATTTTTAAATGATGTTTGTATTATTAAAATTAGCAATTAAGCTCTGAAAATTC[C/T]
AATAAAATTTTAACGAGTGTAACTAATCATGGAGAATTTAAAAAAATTAAATTTAACCATGTCATTTTATTTCTCACACTTGCTTTACTTGTAAATTTAT

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	67.20%	32.50%	0.34%	0.00%	NA
All Indica	2759	97.00%	2.50%	0.47%	0.00%	NA
All Japonica	1512	11.60%	88.40%	0.00%	0.00%	NA
Aus	269	95.90%	4.10%	0.00%	0.00%	NA
Indica I	595	98.00%	0.70%	1.34%	0.00%	NA
Indica II	465	96.60%	3.20%	0.22%	0.00%	NA
Indica III	913	98.20%	1.60%	0.11%	0.00%	NA
Indica Intermediate	786	95.00%	4.60%	0.38%	0.00%	NA
Temperate Japonica	767	2.50%	97.50%	0.00%	0.00%	NA
Tropical Japonica	504	29.00%	71.00%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	16.70%	83.30%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	3.33%	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
vg0624615989	G -> A	LOC_Os06g41140-LOC_Os06g41150	intergenic_region ; MODIFIER	silent_mutation	Average:23.069; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0624615989	NA	1.72E-18	mr1077	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
vg0624615989	NA	5.60E-29	mr1256	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
vg0624615989	NA	4.70E-08	mr1583	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
vg0624615989	NA	1.01E-37	mr1601	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
vg0624615989	NA	2.10E-08	mr1623_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
vg0624615989	NA	2.85E-36	mr1689_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
vg0624615989	1.13E-10	NA	mr1850_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
vg0624615989	4.84E-07	3.78E-09	mr1850_2	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