Search for Variation information by Variation ID:

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

Detailed information for vg1012428033:

Variant ID: vg1012428033 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 12428033
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.85, A: 0.16, others allele: 0.00, population size: 55. )

Flanking Sequence (100 bp) in Reference Genome:

CAGGCCACACCTGAAAATATGGGCTGCAGACATATTAGACCTAGGCCAAAAAAATATGTCTTCGACTCCCTTTAAAGGATGACGCATGTAACATGCTCCC[G/A]
AGTAATAAATCTTCCGGGTGATACAGACCAAGTGTAGCTCATATCAATAGCTTCTGATCTGAGTGATTATCCCTTATGGGATACTCCAAAATAGATATAA

Reverse complement sequence

TTATATCTATTTTGGAGTATCCCATAAGGGATAATCACTCAGATCAGAAGCTATTGATATGAGCTACACTTGGTCTGTATCACCCGGAAGATTTATTACT[C/T]
GGGAGCATGTTACATGCGTCATCCTTTAAAGGGAGTCGAAGACATATTTTTTTGGCCTAGGTCTAATATGTCTGCAGCCCATATTTTCAGGTGTGGCCTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.10%	44.30%	0.59%	0.00%	NA
All Indica	2759	29.80%	69.30%	0.91%	0.00%	NA
All Japonica	1512	89.80%	10.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	7.10%	92.30%	0.67%	0.00%	NA
Indica II	465	37.00%	62.20%	0.86%	0.00%	NA
Indica III	913	34.50%	64.30%	1.20%	0.00%	NA
Indica Intermediate	786	37.20%	62.10%	0.76%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	81.00%	19.00%	0.00%	0.00%	NA
Japonica Intermediate	241	83.40%	16.20%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	70.00%	27.80%	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
vg1012428033	G -> A	LOC_Os10g24250.1	upstream_gene_variant ; 3521.0bp to feature; MODIFIER	silent_mutation	Average:33.897; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N
vg1012428033	G -> A	LOC_Os10g24250-LOC_Os10g24260	intergenic_region ; MODIFIER	silent_mutation	Average:33.897; most accessible tissue: Zhenshan97 flag leaf, score: 48.165	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1012428033	NA	9.79E-07	mr1053	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
vg1012428033	7.45E-07	6.74E-08	mr1157	Ind_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
vg1012428033	7.70E-08	3.84E-10	mr1328	Ind_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
vg1012428033	1.23E-07	9.95E-10	mr1446	Ind_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
vg1012428033	NA	1.91E-08	mr1827	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
vg1012428033	3.05E-07	NA	mr1446_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
vg1012428033	2.23E-07	1.02E-10	mr1446_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
vg1012428033	NA	7.59E-06	mr1567_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
vg1012428033	NA	5.68E-06	mr1840_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