Search for Variation information by Variation ID:

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

Detailed information for vg0311038848:

Variant ID: vg0311038848 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11038848
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

TAGTGTCAGATCAGGCTTGTATATTTCCTTTCGTCTTTAAGAAACATGTGTCGTGTCCGATATGGACTAGTCACCCATGGATATAAATATGTACGCCCGG[G/A]
GTCTTTGTAATCTATCTCTCGATCAATACAACTACTCTTGGTGCATCGTCACTCTCTTTTCCGAGGTTTTTTTTTATCACCAGCGGAACTTGGCAACTGA

Reverse complement sequence

TCAGTTGCCAAGTTCCGCTGGTGATAAAAAAAAACCTCGGAAAAGAGAGTGACGATGCACCAAGAGTAGTTGTATTGATCGAGAGATAGATTACAAAGAC[C/T]
CCGGGCGTACATATTTATATCCATGGGTGACTAGTCCATATCGGACACGACACATGTTTCTTAAAGACGAAAGGAAATATACAAGCCTGATCTGACACTA

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	96.40%	2.70%	0.93%	0.00%	NA
All Indica	2759	98.90%	0.40%	0.72%	0.00%	NA
All Japonica	1512	90.90%	7.60%	1.46%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	98.00%	0.00%	2.02%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.10%	0.90%	0.00%	0.00%	NA
Indica Intermediate	786	98.60%	0.40%	1.02%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	76.60%	20.00%	3.37%	0.00%	NA
Japonica Intermediate	241	92.10%	5.80%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	97.80%	2.20%	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
vg0311038848	G -> A	LOC_Os03g19610.1	upstream_gene_variant ; 3306.0bp to feature; MODIFIER	silent_mutation	Average:39.12; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0311038848	G -> A	LOC_Os03g19620.1	downstream_gene_variant ; 1551.0bp to feature; MODIFIER	silent_mutation	Average:39.12; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0311038848	G -> A	LOC_Os03g19630.1	downstream_gene_variant ; 946.0bp to feature; MODIFIER	silent_mutation	Average:39.12; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0311038848	G -> A	LOC_Os03g19620-LOC_Os03g19630	intergenic_region ; MODIFIER	silent_mutation	Average:39.12; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311038848	2.40E-06	2.40E-06	mr1266	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