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Detailed information for vg0402455074:

Variant ID: vg0402455074 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 2455074
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCAACCATAAGTCAAAGCTGAAACAGACATGTCCGTTTGCACATAAAGCGACCAAATTAACACTTGACTAATCAAGTACTCCTTCCGTTAAAAAAAAT[C/T]
AACTAAACATACTCATACTCATGTCCAGATTCGTTGTATTAGGCTATATCTCATCTTTATCTATGTTTTTTTATGGACGGGAATATATCGTATAAAATGA

Reverse complement sequence

TCATTTTATACGATATATTCCCGTCCATAAAAAAACATAGATAAAGATGAGATATAGCCTAATACAACGAATCTGGACATGAGTATGAGTATGTTTAGTT[G/A]
ATTTTTTTTAACGGAAGGAGTACTTGATTAGTCAAGTGTTAATTTGGTCGCTTTATGTGCAAACGGACATGTCTGTTTCAGCTTTGACTTATGGTTGAGT

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 63.20% 36.70% 0.04% 0.00% NA
All Indica  2759 54.70% 45.30% 0.04% 0.00% NA
All Japonica  1512 87.80% 12.10% 0.07% 0.00% NA
Aus  269 23.40% 76.60% 0.00% 0.00% NA
Indica I  595 44.70% 55.10% 0.17% 0.00% NA
Indica II  465 36.10% 63.90% 0.00% 0.00% NA
Indica III  913 71.10% 28.90% 0.00% 0.00% NA
Indica Intermediate  786 54.10% 45.90% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 66.90% 33.10% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.40% 0.41% 0.00% NA
VI/Aromatic  96 41.70% 58.30% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 0.00% 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
vg0402455074 C -> T LOC_Os04g05040.1 upstream_gene_variant ; 4050.0bp to feature; MODIFIER silent_mutation Average:59.792; most accessible tissue: Callus, score: 99.052 N N N N
vg0402455074 C -> T LOC_Os04g05040-LOC_Os04g05050 intergenic_region ; MODIFIER silent_mutation Average:59.792; most accessible tissue: Callus, score: 99.052 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0402455074 5.95E-06 3.01E-08 mr1798 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
vg0402455074 2.62E-11 NA mr1798_2 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
vg0402455074 2.93E-06 1.68E-09 mr1798_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
vg0402455074 7.35E-08 8.64E-13 mr1798_2 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