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Detailed information for vg0114039871:

Variant ID: vg0114039871 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 14039871
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:


CTCCCTTCAATTTTAAGTTGTTTACTGATATTATTCTTTTTCTTATGTTGGTTTTAACTTACATTTCTCAGGTTGCACTTGGTGAAATGAATGAACTACT[A/G]
TATGGAGATTTTGGTGCCGATAACCTGCCAAATGGAAAACTAAGGTCAGTTTCTCACACAATTATTTCCAAGTACTTTTCATGGACTTGTGGCATCAACT

Reverse complement sequence

AGTTGATGCCACAAGTCCATGAAAAGTACTTGGAAATAATTGTGTGAGAAACTGACCTTAGTTTTCCATTTGGCAGGTTATCGGCACCAAAATCTCCATA[T/C]
AGTAGTTCATTCATTTCACCAAGTGCAACCTGAGAAATGTAAGTTAAAACCAACATAAGAAAAAGAATAATATCAGTAAACAACTTAAAATTGAAGGGAG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.00% 2.80% 0.25% 0.00% NA
All Indica  2759 96.20% 3.40% 0.36% 0.00% NA
All Japonica  1512 97.40% 2.40% 0.13% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 88.10% 11.10% 0.84% 0.00% NA
Indica II  465 97.60% 2.40% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 1.90% 0.64% 0.00% NA
Temperate Japonica  767 98.40% 1.40% 0.13% 0.00% NA
Tropical Japonica  504 95.20% 4.80% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 0.80% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg0114039871 A -> G LOC_Os01g24920.1 downstream_gene_variant ; 1083.0bp to feature; MODIFIER silent_mutation Average:42.661; most accessible tissue: Callus, score: 65.398 N N N N
vg0114039871 A -> G LOC_Os01g24930.1 downstream_gene_variant ; 3218.0bp to feature; MODIFIER silent_mutation Average:42.661; most accessible tissue: Callus, score: 65.398 N N N N
vg0114039871 A -> G LOC_Os01g24920-LOC_Os01g24930 intergenic_region ; MODIFIER silent_mutation Average:42.661; most accessible tissue: Callus, score: 65.398 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0114039871 NA 1.71E-06 mr1064 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
vg0114039871 4.09E-07 7.09E-10 mr1679 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
vg0114039871 NA 2.23E-06 mr1693 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