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Detailed information for vg0506100456:

Variant ID: vg0506100456 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6100456
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: 304. )

Flanking Sequence (100 bp) in Reference Genome:


CATGATGTTCAGGCCAAACTCTTGTATAGGCATTTGCTTGATCAGATACCTACCCCAGTAGGACTCATGCAAAGATACCTTCTGTGAGTGCAGTTTATAG[G/A]
ATTGAGAGGTATTGGGATCTTAGCCTCAACAAATCAACCCTCCACGAGTGCTTGGGAATTCAAAGTAAATTAAAAGAGAGTTAAAATGGAGTTGCAAAAC

Reverse complement sequence

GTTTTGCAACTCCATTTTAACTCTCTTTTAATTTACTTTGAATTCCCAAGCACTCGTGGAGGGTTGATTTGTTGAGGCTAAGATCCCAATACCTCTCAAT[C/T]
CTATAAACTGCACTCACAGAAGGTATCTTTGCATGAGTCCTACTGGGGTAGGTATCTGATCAAGCAAATGCCTATACAAGAGTTTGGCCTGAACATCATG

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 88.50% 10.70% 0.80% 0.00% NA
All Indica  2759 80.80% 18.00% 1.23% 0.00% NA
All Japonica  1512 99.50% 0.20% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.00% 14.50% 2.52% 0.00% NA
Indica II  465 69.20% 29.20% 1.51% 0.00% NA
Indica III  913 85.90% 14.10% 0.00% 0.00% NA
Indica Intermediate  786 80.00% 18.40% 1.53% 0.00% NA
Temperate Japonica  767 99.50% 0.10% 0.39% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0506100456 G -> A LOC_Os05g10940-LOC_Os05g10950 intergenic_region ; MODIFIER silent_mutation Average:45.398; most accessible tissue: Minghui63 flower, score: 56.663 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506100456 1.36E-06 5.87E-28 mr1039 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
vg0506100456 NA 2.26E-13 mr1039 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
vg0506100456 2.14E-09 2.25E-28 mr1039_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
vg0506100456 7.75E-07 8.46E-13 mr1039_2 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
vg0506100456 3.08E-08 NA mr1632_2 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
vg0506100456 2.53E-06 9.05E-10 mr1632_2 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