Search for Variation information by Variation ID:

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

Detailed information for vg0507386923:

Variant ID: vg0507386923 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7386923
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, C: 0.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGGTCCAAATTTACCCCTAGCTAGTTCCAGGGATTTTGGTCCACGCAGAAACTGATCTTTTTCAATCTCTACTTGATACTTGAATAATGTCTCGGGGA[A/C]
ATTTAATTTAGTTTCAAAACCCTGATGCCTGCAGGGTCTAAATTATAAAAACATTTCCATAGTAGAACATAAACACAGAAAAAGAAAATGGAGAAGAACT

Reverse complement sequence

AGTTCTTCTCCATTTTCTTTTTCTGTGTTTATGTTCTACTATGGAAATGTTTTTATAATTTAGACCCTGCAGGCATCAGGGTTTTGAAACTAAATTAAAT[T/G]
TCCCCGAGACATTATTCAAGTATCAAGTAGAGATTGAAAAAGATCAGTTTCTGCGTGGACCAAAATCCCTGGAACTAGCTAGGGGTAAATTTGGACCCCG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	66.10%	33.60%	0.25%	0.08%	NA
All Indica	2759	79.80%	19.80%	0.29%	0.14%	NA
All Japonica	1512	36.80%	63.00%	0.13%	0.00%	NA
Aus	269	84.80%	15.20%	0.00%	0.00%	NA
Indica I	595	98.80%	1.20%	0.00%	0.00%	NA
Indica II	465	52.90%	46.20%	0.65%	0.22%	NA
Indica III	913	78.00%	21.60%	0.33%	0.11%	NA
Indica Intermediate	786	83.30%	16.20%	0.25%	0.25%	NA
Temperate Japonica	767	52.40%	47.60%	0.00%	0.00%	NA
Tropical Japonica	504	21.20%	78.60%	0.20%	0.00%	NA
Japonica Intermediate	241	19.90%	79.70%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	58.90%	38.90%	2.22%	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
vg0507386923	A -> DEL	N	N	silent_mutation	Average:71.895; most accessible tissue: Zhenshan97 flower, score: 82.948	N	N	N	N
vg0507386923	A -> C	LOC_Os05g13320-LOC_Os05g13330	intergenic_region ; MODIFIER	silent_mutation	Average:71.895; most accessible tissue: Zhenshan97 flower, score: 82.948	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507386923	5.67E-06	1.41E-11	mr1039	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
vg0507386923	NA	6.46E-10	mr1593	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
vg0507386923	NA	1.26E-15	mr1593	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
vg0507386923	9.50E-09	6.06E-13	mr1039_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
vg0507386923	NA	1.68E-06	mr1188_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
vg0507386923	NA	4.22E-08	mr1378_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
vg0507386923	NA	9.54E-06	mr1428_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
vg0507386923	NA	3.08E-06	mr1452_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
vg0507386923	NA	9.68E-13	mr1593_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
vg0507386923	NA	3.05E-15	mr1593_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
vg0507386923	4.05E-08	1.83E-09	mr1632_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
vg0507386923	NA	6.97E-06	mr1875_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
vg0507386923	NA	7.24E-07	mr1942_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