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Detailed information for vg0506970223:

Variant ID: vg0506970223 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6970223
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:


CCTGCCGTCCTGCCTCATTGGTTCCTATGCTATAAGATCTTTTCTTTCTCTGTTTATCTGGTAAGAATAAGGAGGAAGAGAGGGTCTAGCAGCCTAGCAC[G/A]
GTGAGAACTGAGAAGGGGTTGACCTGTTTGTGTGGTTATGCTAGCTTGGAACCTGCTATGCGTTGGACATATATCAAAGTATTGCTACTGTATCAGCTTT

Reverse complement sequence

AAAGCTGATACAGTAGCAATACTTTGATATATGTCCAACGCATAGCAGGTTCCAAGCTAGCATAACCACACAAACAGGTCAACCCCTTCTCAGTTCTCAC[C/T]
GTGCTAGGCTGCTAGACCCTCTCTTCCTCCTTATTCTTACCAGATAAACAGAGAAAGAAAAGATCTTATAGCATAGGAACCAATGAGGCAGGACGGCAGG

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 84.70% 11.30% 4.02% 0.00% NA
All Indica  2759 74.50% 18.90% 6.60% 0.00% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 82.90% 3.50% 13.61% 0.00% NA
Indica II  465 78.10% 17.60% 4.30% 0.00% NA
Indica III  913 71.60% 26.90% 1.42% 0.00% NA
Indica Intermediate  786 69.30% 22.00% 8.65% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.40% 0.20% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 8.90% 7.78% 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
vg0506970223 G -> A LOC_Os05g12170-LOC_Os05g12180 intergenic_region ; MODIFIER silent_mutation Average:64.886; most accessible tissue: Zhenshan97 panicle, score: 75.67 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506970223 4.03E-07 NA mr1593 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
vg0506970223 1.59E-06 6.53E-07 mr1593 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
vg0506970223 7.60E-08 NA mr1593_2 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
vg0506970223 2.57E-07 5.04E-08 mr1593_2 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