Search for Variation information by Variation ID:

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

Detailed information for vg0430466693:

Variant ID: vg0430466693 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 30466693
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ACATAAGCCAAATAAGCCATGATATCAAGAAGAATGATTATGACTTGTGAGGATGACAAGCATCCAATAACCATACATAACTACTAGACTTGTATATATC[C/A]
ACATGCACATAAAGTTACAACAAGCTAGATGAACGCCTCGCAAAATTCTTGCTTTTATTTCTAAAATTATAGTTGTATCTCTTATATAGTTAATATGTAC

Reverse complement sequence

GTACATATTAACTATATAAGAGATACAACTATAATTTTAGAAATAAAAGCAAGAATTTTGCGAGGCGTTCATCTAGCTTGTTGTAACTTTATGTGCATGT[G/T]
GATATATACAAGTCTAGTAGTTATGTATGGTTATTGGATGCTTGTCATCCTCACAAGTCATAATCATTCTTCTTGATATCATGGCTTATTTGGCTTATGT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	92.90%	7.00%	0.02%	0.00%	NA
All Indica	2759	99.10%	0.80%	0.04%	0.00%	NA
All Japonica	1512	79.80%	20.20%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	98.70%	1.30%	0.00%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	1.30%	0.13%	0.00%	NA
Temperate Japonica	767	95.00%	5.00%	0.00%	0.00%	NA
Tropical Japonica	504	68.80%	31.20%	0.00%	0.00%	NA
Japonica Intermediate	241	54.40%	45.60%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	0.00%	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
vg0430466693	C -> A	LOC_Os04g51430.1	downstream_gene_variant ; 3353.0bp to feature; MODIFIER	silent_mutation	Average:37.548; most accessible tissue: Callus, score: 68.009	N	N	N	N
vg0430466693	C -> A	LOC_Os04g51440.1	intron_variant ; MODIFIER	silent_mutation	Average:37.548; most accessible tissue: Callus, score: 68.009	N	N	N	N
vg0430466693	C -> A	LOC_Os04g51440.2	intron_variant ; MODIFIER	silent_mutation	Average:37.548; most accessible tissue: Callus, score: 68.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0430466693	1.54E-06	NA	mr1064	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
vg0430466693	NA	1.24E-08	mr1064	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
vg0430466693	1.14E-06	NA	mr1534	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
vg0430466693	NA	2.45E-09	mr1534	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
vg0430466693	2.65E-12	NA	mr1745	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
vg0430466693	6.05E-06	7.89E-11	mr1745	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
vg0430466693	9.16E-07	NA	mr1042_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
vg0430466693	NA	3.52E-07	mr1042_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
vg0430466693	8.60E-09	NA	mr1064_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
vg0430466693	2.58E-07	4.24E-12	mr1064_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
vg0430466693	NA	5.38E-08	mr1502_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
vg0430466693	NA	5.00E-11	mr1680_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
vg0430466693	NA	3.52E-06	mr1680_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
vg0430466693	NA	6.99E-07	mr1687_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
vg0430466693	4.44E-24	NA	mr1745_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
vg0430466693	3.26E-10	6.00E-20	mr1745_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
vg0430466693	8.17E-07	NA	mr1871_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