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Detailed information for vg0130953874:

Variant ID: vg0130953874 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 30953874
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


CTTTATACACTCCAACACATGCTCCTTCCTATCTGAGGTGATCTCAAGCAAGAAATGAACTGTTAAATCCAGTTCAATATAGCTGATTACTATGTAATGG[G/A]
CAAGCATCTCTGTTCCTCCCTCATTAAATAACGCTGCATCTATAAATTATTAGACCAATTAATTTCACCATGTTCATGAAATAAATGGTAAATTCTCGGT

Reverse complement sequence

ACCGAGAATTTACCATTTATTTCATGAACATGGTGAAATTAATTGGTCTAATAATTTATAGATGCAGCGTTATTTAATGAGGGAGGAACAGAGATGCTTG[C/T]
CCATTACATAGTAATCAGCTATATTGAACTGGATTTAACAGTTCATTTCTTGCTTGAGATCACCTCAGATAGGAAGGAGCATGTGTTGGAGTGTATAAAG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.20% 0.76% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 91.40% 6.40% 2.18% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.10% 1.00% 1.83% 0.00% NA
Tropical Japonica  504 81.50% 15.30% 3.17% 0.00% NA
Japonica Intermediate  241 93.80% 5.00% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 6.70% 3.33% 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
vg0130953874 G -> A LOC_Os01g53850.1 downstream_gene_variant ; 1587.0bp to feature; MODIFIER silent_mutation Average:67.773; most accessible tissue: Minghui63 flower, score: 84.058 N N N N
vg0130953874 G -> A LOC_Os01g53840.1 intron_variant ; MODIFIER silent_mutation Average:67.773; most accessible tissue: Minghui63 flower, score: 84.058 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0130953874 NA 3.33E-06 mr1155 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
vg0130953874 NA 2.18E-06 mr1156 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
vg0130953874 NA 4.58E-07 mr1155_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
vg0130953874 1.75E-07 NA mr1200_2 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