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Detailed information for vg0905280002:

Variant ID: vg0905280002 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5280002
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGGCGCTGGATCTTGGCTATTGTCTGCTATGGAGTAGTACTACTGAACCTGGACCCACTTAAAACCCATTTGAAAGGCAACTAGCACTGTCAGAGCTGT[G/A]
ACCCAAACCTTCACTAGGCCTATTCGGCACACGAAGTTCCAATAGTGCATACAACGTGTCAAGAAGCAAAAGCAGAATCAGAGAAGAAGATGATATCAAT

Reverse complement sequence

ATTGATATCATCTTCTTCTCTGATTCTGCTTTTGCTTCTTGACACGTTGTATGCACTATTGGAACTTCGTGTGCCGAATAGGCCTAGTGAAGGTTTGGGT[C/T]
ACAGCTCTGACAGTGCTAGTTGCCTTTCAAATGGGTTTTAAGTGGGTCCAGGTTCAGTAGTACTACTCCATAGCAGACAATAGCCAAGATCCAGCGCCGT

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 98.10% 1.90% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 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 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 32.30% 67.70% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg0905280002 G -> A LOC_Os09g09760.1 upstream_gene_variant ; 1418.0bp to feature; MODIFIER silent_mutation Average:72.401; most accessible tissue: Callus, score: 87.0 N N N N
vg0905280002 G -> A LOC_Os09g09750.1 downstream_gene_variant ; 1075.0bp to feature; MODIFIER silent_mutation Average:72.401; most accessible tissue: Callus, score: 87.0 N N N N
vg0905280002 G -> A LOC_Os09g09750-LOC_Os09g09760 intergenic_region ; MODIFIER silent_mutation Average:72.401; most accessible tissue: Callus, score: 87.0 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905280002 3.29E-06 3.29E-06 mr1008 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
vg0905280002 1.60E-06 1.60E-06 mr1009 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