Search for Variation information by Variation ID:

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

Detailed information for vg0126439526:

Variant ID: vg0126439526 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 26439526
Reference Allele: T	Alternative Allele: C,A
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, C: 0.04, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AGCTTGAGCATCACCAGAGCCCATCAATTGAAAGACCGCTCAGAAGCTGCCTGCGCTGGTCGTGATGTACAGAAGGGTTAGATTCATATATTGAGTAAAT[T/C,A]
TCAGAAAACTATAACTTTAGTGATAAAATTATCAGTTTGCTGCAACATTAGCGATATATTTCAGTTTGCTGCAACATTAGCGACATATTTCAGTTTGCTA

Reverse complement sequence

TAGCAAACTGAAATATGTCGCTAATGTTGCAGCAAACTGAAATATATCGCTAATGTTGCAGCAAACTGATAATTTTATCACTAAAGTTATAGTTTTCTGA[A/G,T]
ATTTACTCAATATATGAATCTAACCCTTCTGTACATCACGACCAGCGCAGGCAGCTTCTGAGCGGTCTTTCAATTGATGGGCTCTGGTGATGCTCAAGCT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.20%	6.20%	0.00%	0.00%	A: 0.53%
All Indica	2759	96.30%	3.30%	0.00%	0.00%	A: 0.47%
All Japonica	1512	87.50%	12.50%	0.00%	0.00%	NA
Aus	269	95.20%	0.40%	0.00%	0.00%	A: 4.46%
Indica I	595	95.30%	4.40%	0.00%	0.00%	A: 0.34%
Indica II	465	98.30%	1.70%	0.00%	0.00%	NA
Indica III	913	95.70%	3.60%	0.00%	0.00%	A: 0.66%
Indica Intermediate	786	96.40%	2.90%	0.00%	0.00%	A: 0.64%
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	66.70%	33.30%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0126439526	T -> A	LOC_Os01g46470-LOC_Os01g46490	intergenic_region ; MODIFIER	silent_mutation	Average:60.898; most accessible tissue: Callus, score: 94.087	N	N	N	N
vg0126439526	T -> C	LOC_Os01g46470-LOC_Os01g46490	intergenic_region ; MODIFIER	silent_mutation	Average:60.898; most accessible tissue: Callus, score: 94.087	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0126439526	NA	3.74E-07	mr1206	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
vg0126439526	NA	2.48E-07	mr1206	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
vg0126439526	2.99E-06	2.99E-06	mr1208	Jap_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
vg0126439526	NA	1.08E-06	mr1248	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
vg0126439526	NA	2.77E-06	mr1359	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
vg0126439526	9.81E-06	3.07E-08	mr1596	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
vg0126439526	NA	5.12E-06	mr1596	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
vg0126439526	NA	3.29E-07	mr1668	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
vg0126439526	NA	1.43E-14	mr1410_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