Search for Variation information by Variation ID:

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

Detailed information for vg0315426336:

Variant ID: vg0315426336 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15426336
Reference Allele: C	Alternative Allele: G
Primary Allele: C	Secondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

CCAAAGTTTTTTTTTCCAAACTTTTAACTTTTCATCGCATCAAACCTTTCATAAACATACATAACTTTTCAGTCACATCGTTTCTAATTTCAACCAAATT[C/G]
TAAACTTTGGACCAATCTAAACTGAAGAAGATGCTTTTGTACTGTGACCACATATATTTCAGCAGTGTCATTATTAGTTTGCGTTGCAAAGCTACAACAC

Reverse complement sequence

GTGTTGTAGCTTTGCAACGCAAACTAATAATGACACTGCTGAAATATATGTGGTCACAGTACAAAAGCATCTTCTTCAGTTTAGATTGGTCCAAAGTTTA[G/C]
AATTTGGTTGAAATTAGAAACGATGTGACTGAAAAGTTATGTATGTTTATGAAAGGTTTGATGCGATGAAAAGTTAAAAGTTTGGAAAAAAAAACTTTGG

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	73.20%	22.70%	4.10%	0.00%	NA
All Indica	2759	55.50%	37.90%	6.63%	0.00%	NA
All Japonica	1512	98.60%	0.90%	0.53%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	70.30%	18.70%	11.09%	0.00%	NA
Indica II	465	76.80%	16.80%	6.45%	0.00%	NA
Indica III	913	37.50%	61.30%	1.20%	0.00%	NA
Indica Intermediate	786	52.50%	37.80%	9.67%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	96.80%	2.20%	0.99%	0.00%	NA
Japonica Intermediate	241	98.80%	0.40%	0.83%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	85.60%	11.10%	3.33%	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
vg0315426336	C -> G	LOC_Os03g26970.1	downstream_gene_variant ; 1612.0bp to feature; MODIFIER	silent_mutation	Average:65.338; most accessible tissue: Zhenshan97 flower, score: 79.85	N	N	N	N
vg0315426336	C -> G	LOC_Os03g26970-LOC_Os03g26980	intergenic_region ; MODIFIER	silent_mutation	Average:65.338; most accessible tissue: Zhenshan97 flower, score: 79.85	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315426336	9.10E-06	NA	mr1542	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
vg0315426336	NA	2.17E-09	mr1542	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
vg0315426336	2.54E-07	NA	mr1542_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
vg0315426336	9.42E-07	3.88E-12	mr1542_2	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