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Detailed information for vg0225424171:

Variant ID: vg0225424171 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25424171
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.79, A: 0.21, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CTTGCCGCGGCCGGAGTACTGATCCGTGTATCCGGCGGGGAGGCCGGCTCGCCACGACGGGTCGTCCTTGAGGACCCACAGGAACGGCCGGCCGGTGGCC[T/A]
CCAGGCCGACGGCGAGCTCGGTGATCTCGCCCGGCGCGATCGGCGCGACCCATGTCCCGAACGAGACGTACGCCACCGAACCTGGACGCTGCTGGTCGAG

Reverse complement sequence

CTCGACCAGCAGCGTCCAGGTTCGGTGGCGTACGTCTCGTTCGGGACATGGGTCGCGCCGATCGCGCCGGGCGAGATCACCGAGCTCGCCGTCGGCCTGG[A/T]
GGCCACCGGCCGGCCGTTCCTGTGGGTCCTCAAGGACGACCCGTCGTGGCGAGCCGGCCTCCCCGCCGGATACACGGATCAGTACTCCGGCCGCGGCAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 75.90% 24.00% 0.02% 0.00% NA
All Indica  2759 74.20% 25.80% 0.04% 0.00% NA
All Japonica  1512 75.50% 24.50% 0.00% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 43.50% 56.30% 0.17% 0.00% NA
Indica II  465 73.80% 26.20% 0.00% 0.00% NA
Indica III  913 92.10% 7.90% 0.00% 0.00% NA
Indica Intermediate  786 76.70% 23.30% 0.00% 0.00% NA
Temperate Japonica  767 80.30% 19.70% 0.00% 0.00% NA
Tropical Japonica  504 62.50% 37.50% 0.00% 0.00% NA
Japonica Intermediate  241 87.60% 12.40% 0.00% 0.00% NA
VI/Aromatic  96 71.90% 28.10% 0.00% 0.00% NA
Intermediate  90 78.90% 21.10% 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
vg0225424171 T -> A LOC_Os02g42280.1 missense_variant ; p.Glu361Val; MODERATE nonsynonymous_codon ; E361V Average:73.44; most accessible tissue: Zhenshan97 young leaf, score: 86.852 possibly damaging 1.864 DELETERIOUS 0.00

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225424171 NA 3.77E-07 mr1069 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
vg0225424171 NA 7.73E-07 mr1074 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
vg0225424171 NA 1.50E-07 mr1077 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
vg0225424171 NA 6.69E-06 mr1148 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
vg0225424171 NA 8.45E-07 mr1074_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
vg0225424171 NA 9.60E-06 mr1148_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
vg0225424171 NA 5.32E-06 mr1150_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
vg0225424171 NA 1.72E-06 mr1222_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
vg0225424171 NA 5.85E-10 mr1558_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
vg0225424171 NA 7.18E-06 mr1918_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