Search for Variation information by Variation ID:

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

Detailed information for vg0919745618:

Variant ID: vg0919745618 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 19745618
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TAGGAATGCCAAGGTAACGGAATGGAAAAGAACCAACCTCACATTGAAAAAGGTTAGTATATTGATCATGAGCTGTTTGGGCTTCACCAAAGCAGTAAAG[C/G]
TCGCTCTTATGAAAATTAATCTTTAAGCCAGATAATTCTTCGAAAACGTTCAACAACATTTTCAGATTACAAGCTTTCTCTAGATCATGTTCCATAAAGA

Reverse complement sequence

TCTTTATGGAACATGATCTAGAGAAAGCTTGTAATCTGAAAATGTTGTTGAACGTTTTCGAAGAATTATCTGGCTTAAAGATTAATTTTCATAAGAGCGA[G/C]
CTTTACTGCTTTGGTGAAGCCCAAACAGCTCATGATCAATATACTAACCTTTTTCAATGTGAGGTTGGTTCTTTTCCATTCCGTTACCTTGGCATTCCTA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.20%	3.80%	0.04%	0.00%	NA
All Indica	2759	93.40%	6.50%	0.07%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	91.10%	8.60%	0.34%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	95.90%	4.10%	0.00%	0.00%	NA
Indica Intermediate	786	91.50%	8.50%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0919745618	C -> G	LOC_Os09g33490.1	upstream_gene_variant ; 3467.0bp to feature; MODIFIER	silent_mutation	Average:34.024; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0919745618	C -> G	LOC_Os09g33480-LOC_Os09g33490	intergenic_region ; MODIFIER	silent_mutation	Average:34.024; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0919745618	4.00E-06	4.00E-06	mr1544	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