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Detailed information for vg0123633523:

Variant ID: vg0123633523 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23633523
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AAGAACATCAATGTCAGTCTGCCATCTAAGCCACAATGGAAAGCGCGGCCCCAGCTGACATGATCGGAAAGCTGCGTTTCTTAGTTTGAATGGCGGAGAA[G/A]
AATTTGTATGTATATCTATTTTCAAGAAGTTGTCTGACAAATCCAGATACTTCAGACGAGATAAATGTTCAACATGATCCTTAGAGATTACGCCTTGGAA

Reverse complement sequence

TTCCAAGGCGTAATCTCTAAGGATCATGTTGAACATTTATCTCGTCTGAAGTATCTGGATTTGTCAGACAACTTCTTGAAAATAGATATACATACAAATT[C/T]
TTCTCCGCCATTCAAACTAAGAAACGCAGCTTTCCGATCATGTCAGCTGGGGCCGCGCTTTCCATTGTGGCTTAGATGGCAGACTGACATTGATGTTCTT

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 58.50% 29.80% 0.47% 11.24% NA
All Indica  2759 55.00% 44.40% 0.18% 0.43% NA
All Japonica  1512 58.60% 7.10% 0.93% 33.40% NA
Aus  269 92.90% 7.10% 0.00% 0.00% NA
Indica I  595 91.40% 8.60% 0.00% 0.00% NA
Indica II  465 58.90% 40.00% 0.22% 0.86% NA
Indica III  913 28.60% 71.10% 0.00% 0.33% NA
Indica Intermediate  786 55.70% 43.10% 0.51% 0.64% NA
Temperate Japonica  767 70.80% 0.40% 0.52% 28.29% NA
Tropical Japonica  504 32.30% 16.30% 1.39% 50.00% NA
Japonica Intermediate  241 74.70% 9.10% 1.24% 14.94% NA
VI/Aromatic  96 62.50% 33.30% 1.04% 3.12% NA
Intermediate  90 55.60% 30.00% 2.22% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0123633523 G -> A LOC_Os01g41750.1 missense_variant ; p.Ser618Phe; MODERATE nonsynonymous_codon ; S618F Average:52.955; most accessible tissue: Callus, score: 85.105 benign 0.048 DELETERIOUS 0.01
vg0123633523 G -> DEL LOC_Os01g41750.1 N frameshift_variant Average:52.955; most accessible tissue: Callus, score: 85.105 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123633523 NA 7.62E-07 mr1100 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
vg0123633523 NA 8.69E-06 mr1380 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
vg0123633523 NA 8.25E-09 mr1561 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
vg0123633523 NA 1.66E-06 mr1795 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
vg0123633523 NA 1.09E-07 mr1861 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
vg0123633523 NA 2.08E-07 mr1875 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
vg0123633523 NA 3.52E-08 mr1908 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
vg0123633523 NA 2.03E-07 mr1962 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
vg0123633523 NA 3.13E-08 mr1100_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
vg0123633523 NA 7.64E-13 mr1380_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
vg0123633523 NA 1.34E-09 mr1380_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
vg0123633523 NA 1.40E-14 mr1561_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
vg0123633523 NA 1.50E-10 mr1561_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
vg0123633523 NA 1.84E-07 mr1795_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
vg0123633523 NA 2.55E-13 mr1875_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
vg0123633523 NA 3.05E-08 mr1875_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
vg0123633523 6.89E-06 3.27E-14 mr1908_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
vg0123633523 NA 1.26E-09 mr1908_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
vg0123633523 NA 1.43E-08 mr1962_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
vg0123633523 3.38E-06 2.29E-12 mr1996_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
vg0123633523 NA 3.60E-09 mr1996_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