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Detailed information for vg0424472928:

Variant ID: vg0424472928 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 24472928
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGACGCCCTCTGGGGGAAGGAAGCCCCAGAAGAGGGAGGGCACTGAAAGATGTGGCCGAAGGCCACCCACAATGAGTTTTCTTCAATCAAACTTTATC[G/A]
AGTTGCTTGTTAGATCAACACACTCCAACGTCCTTCAAGGGAAGGAAGCCTAAAAGGAGGGAGAAACGCTGAAAGGTCTTGGACGGTCTCAAGGAAGGGG

Reverse complement sequence

CCCCTTCCTTGAGACCGTCCAAGACCTTTCAGCGTTTCTCCCTCCTTTTAGGCTTCCTTCCCTTGAAGGACGTTGGAGTGTGTTGATCTAACAAGCAACT[C/T]
GATAAAGTTTGATTGAAGAAAACTCATTGTGGGTGGCCTTCGGCCACATCTTTCAGTGCCCTCCCTCTTCTGGGGCTTCCTTCCCCCAGAGGGCGTCGGC

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 99.30% 0.30% 0.38% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 98.00% 0.90% 1.12% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.30% 0.50% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.10% 1.70% 2.22% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 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  90 100.00% 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
vg0424472928 G -> A LOC_Os04g41238.1 3_prime_UTR_variant ; 258.0bp to feature; MODIFIER silent_mutation Average:68.308; most accessible tissue: Callus, score: 90.48 N N N N
vg0424472928 G -> A LOC_Os04g41229.1 downstream_gene_variant ; 3979.0bp to feature; MODIFIER silent_mutation Average:68.308; most accessible tissue: Callus, score: 90.48 N N N N
vg0424472928 G -> A LOC_Os04g41229.2 downstream_gene_variant ; 4609.0bp to feature; MODIFIER silent_mutation Average:68.308; most accessible tissue: Callus, score: 90.48 N N N N
vg0424472928 G -> A LOC_Os04g41250.1 intron_variant ; MODIFIER silent_mutation Average:68.308; most accessible tissue: Callus, score: 90.48 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0424472928 2.00E-07 2.00E-07 mr1915 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
vg0424472928 NA 2.06E-06 mr1129_2 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
vg0424472928 7.12E-06 5.61E-06 mr1255_2 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
vg0424472928 NA 1.27E-06 mr1257_2 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