Search for Variation information by Variation ID:

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

Detailed information for vg1217890002:

Variant ID: vg1217890002 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17890002
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

ACAAATGTATAAATTCCATCAACTGTACATGGAGATGAGCGCCACCGGTAGAGAGATGATCGGAGCGAGGATCAGGGACACGGACTTCTTGCAAGGAGAA[G/A]
ATATTCTCTGGATCAATTTCAAAGGTATCTACGAACTACACCAGCTGGACGCCCTCGACGTCTCTATTATGAGTTGCTGGATTTTGTAAGTATCGTTCAG

Reverse complement sequence

CTGAACGATACTTACAAAATCCAGCAACTCATAATAGAGACGTCGAGGGCGTCCAGCTGGTGTAGTTCGTAGATACCTTTGAAATTGATCCAGAGAATAT[C/T]
TTCTCCTTGCAAGAAGTCCGTGTCCCTGATCCTCGCTCCGATCATCTCTCTACCGGTGGCGCTCATCTCCATGTACAGTTGATGGAATTTATACATTTGT

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	80.90%	6.00%	5.44%	7.64%	NA
All Indica	2759	80.10%	10.10%	5.62%	4.20%	NA
All Japonica	1512	80.80%	0.30%	4.70%	14.22%	NA
Aus	269	93.30%	0.00%	6.32%	0.37%	NA
Indica I	595	58.80%	25.50%	12.77%	2.86%	NA
Indica II	465	87.30%	2.80%	5.59%	4.30%	NA
Indica III	913	86.90%	5.30%	2.74%	5.15%	NA
Indica Intermediate	786	84.10%	8.30%	3.56%	4.07%	NA
Temperate Japonica	767	98.30%	0.10%	0.52%	1.04%	NA
Tropical Japonica	504	61.50%	0.40%	9.92%	28.17%	NA
Japonica Intermediate	241	65.60%	0.40%	7.05%	26.97%	NA
VI/Aromatic	96	59.40%	0.00%	12.50%	28.12%	NA
Intermediate	90	92.20%	3.30%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1217890002	G -> DEL	N	N	silent_mutation	Average:22.111; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1217890002	G -> A	LOC_Os12g29940.1	upstream_gene_variant ; 2072.0bp to feature; MODIFIER	silent_mutation	Average:22.111; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N
vg1217890002	G -> A	LOC_Os12g29920-LOC_Os12g29940	intergenic_region ; MODIFIER	silent_mutation	Average:22.111; most accessible tissue: Zhenshan97 flag leaf, score: 47.303	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217890002	NA	7.85E-06	mr1081	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
vg1217890002	6.90E-07	6.90E-07	mr1194	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
vg1217890002	NA	6.68E-06	mr1864	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