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Detailed information for vg0514649039:

Variant ID: vg0514649039 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14649039
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.91, T: 0.09, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


CTGGTATATTTTGGTTACAGAGTTCATCCGCAAGCGCACGGATATACTATTGTAGCATTTCACCCGAGAGTATTCCAAGGGTATCGTATTTATTTAATCC[T/C]
GTGGAAAGATCATAGTAGAGAGAACCTGACTAATTATTTATATGTTACTTGTAATAATCATAGTCTAAGCAGGGGTTAAGATAAATCCAAAGGTAGAGTG

Reverse complement sequence

CACTCTACCTTTGGATTTATCTTAACCCCTGCTTAGACTATGATTATTACAAGTAACATATAAATAATTAGTCAGGTTCTCTCTACTATGATCTTTCCAC[A/G]
GGATTAAATAAATACGATACCCTTGGAATACTCTCGGGTGAAATGCTACAATAGTATATCCGTGCGCTTGCGGATGAACTCTGTAACCAAAATATACCAG

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 55.20% 44.60% 0.15% 0.00% NA
All Indica  2759 84.20% 15.60% 0.18% 0.00% NA
All Japonica  1512 1.90% 98.00% 0.07% 0.00% NA
Aus  269 81.40% 18.60% 0.00% 0.00% NA
Indica I  595 83.00% 16.60% 0.34% 0.00% NA
Indica II  465 74.80% 25.20% 0.00% 0.00% NA
Indica III  913 89.60% 10.40% 0.00% 0.00% NA
Indica Intermediate  786 84.40% 15.30% 0.38% 0.00% NA
Temperate Japonica  767 2.60% 97.40% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 1.70% 97.90% 0.41% 0.00% NA
VI/Aromatic  96 6.20% 93.80% 0.00% 0.00% NA
Intermediate  90 37.80% 61.10% 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
vg0514649039 T -> C LOC_Os05g25240.1 downstream_gene_variant ; 1041.0bp to feature; MODIFIER silent_mutation Average:29.578; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N
vg0514649039 T -> C LOC_Os05g25240-LOC_Os05g25250 intergenic_region ; MODIFIER silent_mutation Average:29.578; most accessible tissue: Minghui63 panicle, score: 53.77 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514649039 2.21E-07 1.83E-35 mr1039 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
vg0514649039 1.05E-06 1.31E-09 mr1039 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
vg0514649039 NA 7.02E-12 mr1514 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
vg0514649039 NA 6.50E-36 mr1632 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
vg0514649039 NA 2.05E-09 mr1632 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
vg0514649039 2.30E-09 1.03E-38 mr1039_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
vg0514649039 2.91E-07 1.88E-09 mr1039_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
vg0514649039 1.35E-11 3.57E-47 mr1632_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
vg0514649039 1.22E-08 2.46E-11 mr1632_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
vg0514649039 NA 9.65E-35 mr1873_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
vg0514649039 NA 5.68E-06 mr1873_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