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Detailed information for vg0906090072:

Variant ID: vg0906090072 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6090072
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


ACGTGGGCATTCCATGTGTTCCTCCCATTCAAATATATGATGAAATATCCAATTTTCCCTTGCATATATCTTGGAAAGGAGAGAAAAAGAAAAGGAAAAA[G/A]
GGGAATAAAAAGAAAAGAAGTAATTTTTCGTATTAATTTATTTTACAATTTTAACATTCAAATAATGCAACTCTGTACCCGGCATTTGTTTGGCATGCTA

Reverse complement sequence

TAGCATGCCAAACAAATGCCGGGTACAGAGTTGCATTATTTGAATGTTAAAATTGTAAAATAAATTAATACGAAAAATTACTTCTTTTCTTTTTATTCCC[C/T]
TTTTTCCTTTTCTTTTTCTCTCCTTTCCAAGATATATGCAAGGGAAAATTGGATATTTCATCATATATTTGAATGGGAGGAACACATGGAATGCCCACGT

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 74.60% 25.30% 0.04% 0.00% NA
All Indica  2759 99.10% 0.80% 0.07% 0.00% NA
All Japonica  1512 24.80% 75.20% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 98.80% 1.00% 0.17% 0.00% NA
Indica II  465 99.10% 0.90% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.50% 0.13% 0.00% NA
Temperate Japonica  767 15.10% 84.90% 0.00% 0.00% NA
Tropical Japonica  504 24.20% 75.80% 0.00% 0.00% NA
Japonica Intermediate  241 56.80% 43.20% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0906090072 G -> A LOC_Os09g11005.1 downstream_gene_variant ; 3834.0bp to feature; MODIFIER silent_mutation Average:31.999; most accessible tissue: Callus, score: 55.969 N N N N
vg0906090072 G -> A LOC_Os09g11000-LOC_Os09g11005 intergenic_region ; MODIFIER silent_mutation Average:31.999; most accessible tissue: Callus, score: 55.969 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906090072 4.76E-06 NA Awn_length All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652