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Detailed information for vg0324573058:

Variant ID: vg0324573058 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24573058
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.52, T: 0.48, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


TGATTTGTGATGGGACTGTGGCGGGATAAACTTTTGTGCAAGAGTGAAGTACATGGACGGTCTCTAAACTTGTGCCGGTGTGTCATTTAGGTCCCTGAAC[C/T]
CCTAAAATACATTTTTAGGTCTCCGAACTTTGCATGTGTATCATATAGGTCCAAACGGGTTCTAACCCACTCCATGCGCTGATGTGGCAATGCCACGGTA

Reverse complement sequence

TACCGTGGCATTGCCACATCAGCGCATGGAGTGGGTTAGAACCCGTTTGGACCTATATGATACACATGCAAAGTTCGGAGACCTAAAAATGTATTTTAGG[G/A]
GTTCAGGGACCTAAATGACACACCGGCACAAGTTTAGAGACCGTCCATGTACTTCACTCTTGCACAAAAGTTTATCCCGCCACAGTCCCATCACAAATCA

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 54.70% 45.00% 0.15% 0.06% NA
All Indica  2759 83.10% 16.60% 0.22% 0.07% NA
All Japonica  1512 1.00% 99.00% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 0.00% 0.00% NA
Indica I  595 66.20% 33.10% 0.50% 0.17% NA
Indica II  465 97.00% 3.00% 0.00% 0.00% NA
Indica III  913 90.90% 9.00% 0.11% 0.00% NA
Indica Intermediate  786 78.80% 20.90% 0.25% 0.13% NA
Temperate Japonica  767 0.70% 99.30% 0.00% 0.00% NA
Tropical Japonica  504 1.00% 99.00% 0.00% 0.00% NA
Japonica Intermediate  241 2.10% 97.90% 0.00% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 43.30% 54.40% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0324573058 C -> T LOC_Os03g43840.1 downstream_gene_variant ; 1249.0bp to feature; MODIFIER silent_mutation Average:70.771; most accessible tissue: Minghui63 root, score: 81.852 N N N N
vg0324573058 C -> T LOC_Os03g43830-LOC_Os03g43840 intergenic_region ; MODIFIER silent_mutation Average:70.771; most accessible tissue: Minghui63 root, score: 81.852 N N N N
vg0324573058 C -> DEL N N silent_mutation Average:70.771; most accessible tissue: Minghui63 root, score: 81.852 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324573058 NA 1.61E-08 mr1595 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
vg0324573058 NA 4.82E-09 mr1637 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
vg0324573058 NA 1.02E-06 mr1671 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
vg0324573058 NA 6.85E-06 mr1734 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
vg0324573058 5.45E-07 5.45E-07 mr1866 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
vg0324573058 NA 1.87E-07 mr1205_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