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Detailed information for vg0216897057:

Variant ID: vg0216897057 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16897057
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 78. )

Flanking Sequence (100 bp) in Reference Genome:


ATATTATCCGATATGATATACCAATACTTTACTCTCCTGGATCTAAACACCCCTTTCTATAAAAAAAATACACCGTTTAACAGTTTAAAAAGCGTGTGCG[C/T]
GAAAAACAAGGCGAAGTAGCTAGGAACCAGCAGTTCCGATCCCAGCAGTTCCAAACACAGCAATTCTTTTTTAGGGAGTTTTTGCATGCTTCTCCGTCTT

Reverse complement sequence

AAGACGGAGAAGCATGCAAAAACTCCCTAAAAAAGAATTGCTGTGTTTGGAACTGCTGGGATCGGAACTGCTGGTTCCTAGCTACTTCGCCTTGTTTTTC[G/A]
CGCACACGCTTTTTAAACTGTTAAACGGTGTATTTTTTTTATAGAAAGGGGTGTTTAGATCCAGGAGAGTAAAGTATTGGTATATCATATCGGATAATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 93.70% 6.10% 0.25% 0.00% NA
All Indica  2759 97.50% 2.50% 0.00% 0.00% NA
All Japonica  1512 85.60% 13.60% 0.73% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 92.00% 8.00% 0.00% 0.00% NA
Indica III  913 97.90% 2.10% 0.00% 0.00% NA
Indica Intermediate  786 98.20% 1.80% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 0.70% 0.65% 0.00% NA
Tropical Japonica  504 74.40% 25.40% 0.20% 0.00% NA
Japonica Intermediate  241 67.60% 30.30% 2.07% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 90.00% 8.90% 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
vg0216897057 C -> T LOC_Os02g28550.1 downstream_gene_variant ; 4070.0bp to feature; MODIFIER silent_mutation Average:42.446; most accessible tissue: Callus, score: 72.606 N N N N
vg0216897057 C -> T LOC_Os02g28550-LOC_Os02g28560 intergenic_region ; MODIFIER silent_mutation Average:42.446; most accessible tissue: Callus, score: 72.606 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216897057 3.58E-06 3.58E-06 mr1591 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
vg0216897057 NA 6.61E-06 mr1657 Jap_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
vg0216897057 1.67E-06 1.10E-08 mr1890 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
vg0216897057 4.37E-07 4.37E-07 mr1891 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