Search for Variation information by Variation ID:

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

Detailed information for vg0136063153:

Variant ID: vg0136063153 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 36063153
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

GAGATAAGCGGGAAAAAAAGCGCGCTTGCCCGCCCCACTTGCATCCCTAATGCTCAAGGATTCTAGAGGTGAAAATTAGGGATGACAATTGTGCCCGTTT[G/A]
CCCGTTTATCCATGGGTAAAAACCCTATTAGGGTTGGGTTTGTTCTCCATTTTATACCCATGGGTATCTTATTGGGTCAAAAGCTATGCCCGATGGGTAA

Reverse complement sequence

TTACCCATCGGGCATAGCTTTTGACCCAATAAGATACCCATGGGTATAAAATGGAGAACAAACCCAACCCTAATAGGGTTTTTACCCATGGATAAACGGG[C/T]
AAACGGGCACAATTGTCATCCCTAATTTTCACCTCTAGAATCCTTGAGCATTAGGGATGCAAGTGGGGCGGGCAAGCGCGCTTTTTTTCCCGCTTATCTC

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	53.30%	46.10%	0.47%	0.15%	NA
All Indica	2759	27.80%	71.30%	0.72%	0.22%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.00%	NA
Aus	269	42.40%	56.90%	0.74%	0.00%	NA
Indica I	595	14.50%	83.90%	1.34%	0.34%	NA
Indica II	465	6.90%	92.00%	0.86%	0.22%	NA
Indica III	913	41.30%	58.50%	0.11%	0.11%	NA
Indica Intermediate	786	34.60%	64.20%	0.89%	0.25%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	97.40%	2.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	93.80%	6.20%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0136063153	G -> A	LOC_Os01g62310.1	upstream_gene_variant ; 3519.0bp to feature; MODIFIER	silent_mutation	Average:37.863; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0136063153	G -> A	LOC_Os01g62310-LOC_Os01g62320	intergenic_region ; MODIFIER	silent_mutation	Average:37.863; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0136063153	G -> DEL	N	N	silent_mutation	Average:37.863; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0136063153	NA	8.99E-11	mr1581	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
vg0136063153	1.72E-06	9.09E-10	mr1887	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
vg0136063153	NA	4.89E-07	mr1302_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
vg0136063153	NA	2.90E-06	mr1364_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