Search for Variation information by Variation ID:

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

Detailed information for vg0420767744:

Variant ID: vg0420767744 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 20767744
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, T: 0.05, others allele: 0.00, population size: 195. )

Flanking Sequence (100 bp) in Reference Genome:

GTCTAACAAAAAGTATTTCGAGGTACCGATATCTCAAGATACCGAATCGTTTTCAATCGTTGGAGTTAAAAACAATTTTAAAGAGTGAGGTACCGATATC[G/T]
TAAGATATTTTTTTTTCTCACCAGAGCAAATCTCATTGCTCGGCATACTTGCTGCCACTGGCTTCTGCCTTTGCCACAAAGGCACTGCTTCGCAATAATG

Reverse complement sequence

CATTATTGCGAAGCAGTGCCTTTGTGGCAAAGGCAGAAGCCAGTGGCAGCAAGTATGCCGAGCAATGAGATTTGCTCTGGTGAGAAAAAAAAATATCTTA[C/A]
GATATCGGTACCTCACTCTTTAAAATTGTTTTTAACTCCAACGATTGAAAACGATTCGGTATCTTGAGATATCGGTACCTCGAAATACTTTTTGTTAGAC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.30%	12.80%	0.30%	12.61%	NA
All Indica	2759	85.40%	13.40%	0.11%	1.09%	NA
All Japonica	1512	66.50%	0.60%	0.40%	32.54%	NA
Aus	269	4.50%	76.60%	0.74%	18.22%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	81.10%	17.20%	0.00%	1.72%	NA
Indica III	913	78.90%	20.20%	0.11%	0.88%	NA
Indica Intermediate	786	84.60%	13.50%	0.25%	1.65%	NA
Temperate Japonica	767	83.20%	0.10%	0.26%	16.43%	NA
Tropical Japonica	504	40.30%	1.20%	0.79%	57.74%	NA
Japonica Intermediate	241	68.00%	0.80%	0.00%	31.12%	NA
VI/Aromatic	96	79.20%	12.50%	1.04%	7.29%	NA
Intermediate	90	67.80%	10.00%	2.22%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0420767744	G -> DEL	N	N	silent_mutation	Average:59.902; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0420767744	G -> T	LOC_Os04g34290.1	upstream_gene_variant ; 1223.0bp to feature; MODIFIER	silent_mutation	Average:59.902; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0420767744	G -> T	LOC_Os04g34280.1	downstream_gene_variant ; 2356.0bp to feature; MODIFIER	silent_mutation	Average:59.902; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N
vg0420767744	G -> T	LOC_Os04g34280-LOC_Os04g34290	intergenic_region ; MODIFIER	silent_mutation	Average:59.902; most accessible tissue: Zhenshan97 panicle, score: 80.486	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0420767744	NA	3.18E-06	mr1230	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
vg0420767744	NA	1.53E-06	mr1319	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
vg0420767744	NA	5.12E-10	mr1320	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
vg0420767744	NA	3.80E-07	mr1321	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
vg0420767744	NA	6.92E-07	mr1328	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
vg0420767744	NA	1.68E-08	mr1348	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
vg0420767744	NA	4.58E-07	mr1365	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
vg0420767744	NA	1.27E-07	mr1424	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
vg0420767744	NA	4.97E-09	mr1442	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
vg0420767744	NA	1.98E-06	mr1545	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
vg0420767744	NA	5.48E-06	mr1633	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