Search for Variation information by Variation ID:

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

Detailed information for vg0209189237:

Variant ID: vg0209189237 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 9189237
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.80, T: 0.18, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGTCTAATACGAATTATTACATCATAGGCCCGCAGGCATAGTCTTAAATCATCGGACCGAGCGGTCCGGAATACATCCAAAAACAGAAATAGATAAGG[T/C]
AGCGGAATTCAGGCAGCGGCATGCCATTGCCACAGGCAACGACCGTACTAAGACCTACTGGGCACCATCGTCTTCGTCTCCCTCCTGGTAGTAGGCATAG

Reverse complement sequence

CTATGCCTACTACCAGGAGGGAGACGAAGACGATGGTGCCCAGTAGGTCTTAGTACGGTCGTTGCCTGTGGCAATGGCATGCCGCTGCCTGAATTCCGCT[A/G]
CCTTATCTATTTCTGTTTTTGGATGTATTCCGGACCGCTCGGTCCGATGATTTAAGACTATGCCTGCGGGCCTATGATGTAATAATTCGTATTAGACACT

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	46.70%	6.40%	28.80%	18.15%	NA
All Indica	2759	20.20%	3.80%	45.92%	30.08%	NA
All Japonica	1512	98.20%	0.20%	0.99%	0.60%	NA
Aus	269	9.30%	68.40%	20.07%	2.23%	NA
Indica I	595	45.50%	0.70%	35.97%	17.82%	NA
Indica II	465	20.20%	6.50%	41.94%	31.40%	NA
Indica III	913	2.30%	3.60%	55.64%	38.44%	NA
Indica Intermediate	786	21.80%	4.80%	44.53%	28.88%	NA
Temperate Japonica	767	98.30%	0.30%	0.52%	0.91%	NA
Tropical Japonica	504	98.00%	0.00%	1.79%	0.20%	NA
Japonica Intermediate	241	98.30%	0.40%	0.83%	0.41%	NA
VI/Aromatic	96	86.50%	6.20%	7.29%	0.00%	NA
Intermediate	90	61.10%	4.40%	20.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0209189237	T -> DEL	N	N	silent_mutation	Average:11.524; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0209189237	T -> C	LOC_Os02g16150.1	upstream_gene_variant ; 467.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0209189237	T -> C	LOC_Os02g16160.1	upstream_gene_variant ; 2608.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0209189237	T -> C	LOC_Os02g16140.1	downstream_gene_variant ; 3530.0bp to feature; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N
vg0209189237	T -> C	LOC_Os02g16150-LOC_Os02g16160	intergenic_region ; MODIFIER	silent_mutation	Average:11.524; most accessible tissue: Minghui63 root, score: 17.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0209189237	NA	5.57E-13	mr1471	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
vg0209189237	NA	6.67E-12	mr1722	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
vg0209189237	NA	7.80E-08	mr1808	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