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Detailed information for vg0516738677:

Variant ID: vg0516738677 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 16738677
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ATTCGAAAATAAATGCAATAGTTGAATAGAAACAATAGCTTTAAACGGGATCAACATGCTCAAAGGGTTGTTTGGGATCTGTGTGACTTGCCTTGCTGGC[C/T]
TTGGAAGTCTTCAAATTCTTCTCCTGCAAAAACGGACTCTCCAGAAACGTCGGAATCTAAACAGAAAAGAGCAAAATCACCAAAACAGCACACAAACAAG

Reverse complement sequence

CTTGTTTGTGTGCTGTTTTGGTGATTTTGCTCTTTTCTGTTTAGATTCCGACGTTTCTGGAGAGTCCGTTTTTGCAGGAGAAGAATTTGAAGACTTCCAA[G/A]
GCCAGCAAGGCAAGTCACACAGATCCCAAACAACCCTTTGAGCATGTTGATCCCGTTTAAAGCTATTGTTTCTATTCAACTATTGCATTTATTTTCGAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.30% 40.50% 0.19% 0.00% NA
All Indica  2759 91.70% 8.10% 0.22% 0.00% NA
All Japonica  1512 1.80% 98.20% 0.00% 0.00% NA
Aus  269 78.40% 21.60% 0.00% 0.00% NA
Indica I  595 97.80% 1.80% 0.34% 0.00% NA
Indica II  465 74.60% 25.40% 0.00% 0.00% NA
Indica III  913 94.70% 5.00% 0.22% 0.00% NA
Indica Intermediate  786 93.50% 6.20% 0.25% 0.00% NA
Temperate Japonica  767 2.50% 97.50% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.20% 98.80% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 38.90% 57.80% 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
vg0516738677 C -> T LOC_Os05g28590.1 upstream_gene_variant ; 434.0bp to feature; MODIFIER silent_mutation Average:20.46; most accessible tissue: Zhenshan97 flower, score: 30.815 N N N N
vg0516738677 C -> T LOC_Os05g28600.1 upstream_gene_variant ; 3775.0bp to feature; MODIFIER silent_mutation Average:20.46; most accessible tissue: Zhenshan97 flower, score: 30.815 N N N N
vg0516738677 C -> T LOC_Os05g28570.1 downstream_gene_variant ; 4776.0bp to feature; MODIFIER silent_mutation Average:20.46; most accessible tissue: Zhenshan97 flower, score: 30.815 N N N N
vg0516738677 C -> T LOC_Os05g28580.1 downstream_gene_variant ; 2798.0bp to feature; MODIFIER silent_mutation Average:20.46; most accessible tissue: Zhenshan97 flower, score: 30.815 N N N N
vg0516738677 C -> T LOC_Os05g28580-LOC_Os05g28590 intergenic_region ; MODIFIER silent_mutation Average:20.46; most accessible tissue: Zhenshan97 flower, score: 30.815 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0516738677 NA 5.18E-11 mr1281 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
vg0516738677 1.39E-06 NA mr1705 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