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Detailed information for vg0116261925:

Variant ID: vg0116261925 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 16261925
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAAGGAAACAACAATGCCCAGGAACTGTTATTGGAGGACGCCAGTAAAATCACCTGCACCGGCCAAGAAGTCAGAGCAGTCGGCTCAGAAGAAGCCGT[C/T]
TCCCGCACCGAAATCAAAGAAGGTGTGGAGGAAGAAGCCAAAGATGCCCGCTCCATCACCTCCGGAGACGGATGGAAGATCCGTGAACTGAATCGAAAGG

Reverse complement sequence

CCTTTCGATTCAGTTCACGGATCTTCCATCCGTCTCCGGAGGTGATGGAGCGGGCATCTTTGGCTTCTTCCTCCACACCTTCTTTGATTTCGGTGCGGGA[G/A]
ACGGCTTCTTCTGAGCCGACTGCTCTGACTTCTTGGCCGGTGCAGGTGATTTTACTGGCGTCCTCCAATAACAGTTCCTGGGCATTGTTGTTTCCTTTTC

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 93.60% 4.00% 2.43% 0.00% NA
All Indica  2759 90.00% 6.10% 3.91% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 91.80% 6.70% 1.49% 0.00% NA
Indica I  595 73.40% 15.10% 11.43% 0.00% NA
Indica II  465 96.30% 3.20% 0.43% 0.00% NA
Indica III  913 97.00% 2.30% 0.66% 0.00% NA
Indica Intermediate  786 90.60% 5.30% 4.07% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 1.10% 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
vg0116261925 C -> T LOC_Os01g29040.1 upstream_gene_variant ; 3406.0bp to feature; MODIFIER silent_mutation Average:54.821; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N
vg0116261925 C -> T LOC_Os01g29050.1 intron_variant ; MODIFIER silent_mutation Average:54.821; most accessible tissue: Zhenshan97 flag leaf, score: 73.475 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0116261925 1.78E-06 NA mr1519 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
vg0116261925 9.95E-09 1.24E-09 mr1519 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
vg0116261925 1.88E-07 NA mr1519_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
vg0116261925 2.63E-08 1.61E-11 mr1519_2 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
vg0116261925 NA 7.09E-06 mr1874_2 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