Search for Variation information by Variation ID:

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

Detailed information for vg0315534358:

Variant ID: vg0315534358 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15534358
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TGGCACCAAAGTCGCGGAGATGGTGGGCGGTGGGCTAGTGATGACGGCTAGGAAAATCGGAGCTTGTGATTAGGAGGCGGTGGCTAGTAGTGGTGGATCT[G/T]
GCGGTAGGGAGCTGTCGAAGACGGGGAAGACGGCTGGGCGAAGCACTTGCACGTCGGTTTGGGTAAGAAAGGGGGGCGGGGTGGAGGAGGCTAGCTAGGG

Reverse complement sequence

CCCTAGCTAGCCTCCTCCACCCCGCCCCCCTTTCTTACCCAAACCGACGTGCAAGTGCTTCGCCCAGCCGTCTTCCCCGTCTTCGACAGCTCCCTACCGC[C/A]
AGATCCACCACTACTAGCCACCGCCTCCTAATCACAAGCTCCGATTTTCCTAGCCGTCATCACTAGCCCACCGCCCACCATCTCCGCGACTTTGGTGCCA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.10%	6.00%	0.89%	0.00%	NA
All Indica	2759	98.80%	0.20%	1.05%	0.00%	NA
All Japonica	1512	81.00%	18.30%	0.79%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.30%	0.00%	1.68%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.50%	0.40%	0.11%	0.00%	NA
Indica Intermediate	786	97.80%	0.10%	2.04%	0.00%	NA
Temperate Japonica	767	97.70%	2.30%	0.00%	0.00%	NA
Tropical Japonica	504	55.80%	41.90%	2.38%	0.00%	NA
Japonica Intermediate	241	80.50%	19.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0315534358	G -> T	LOC_Os03g27120.1	upstream_gene_variant ; 1899.0bp to feature; MODIFIER	silent_mutation	Average:70.527; most accessible tissue: Zhenshan97 young leaf, score: 90.985	N	N	N	N
vg0315534358	G -> T	LOC_Os03g27140.1	upstream_gene_variant ; 2628.0bp to feature; MODIFIER	silent_mutation	Average:70.527; most accessible tissue: Zhenshan97 young leaf, score: 90.985	N	N	N	N
vg0315534358	G -> T	LOC_Os03g27110.1	downstream_gene_variant ; 4187.0bp to feature; MODIFIER	silent_mutation	Average:70.527; most accessible tissue: Zhenshan97 young leaf, score: 90.985	N	N	N	N
vg0315534358	G -> T	LOC_Os03g27120-LOC_Os03g27140	intergenic_region ; MODIFIER	silent_mutation	Average:70.527; most accessible tissue: Zhenshan97 young leaf, score: 90.985	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315534358	4.73E-06	1.46E-09	mr1715	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
vg0315534358	5.51E-06	9.95E-10	mr1715_2	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