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Detailed information for vg1113429006:

Variant ID: vg1113429006 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13429006
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:


CAAGCAGAAGCAGTAGGATGGAAAGAGTTCCACCTCAGGTATTAATGTTATAGAAATTAATCTTGCTACTTCCTCTACTGATTCTTGGGTATTTGATACC[G/A]
GGTCAGTTGCTCATATATGCAAATCTTTGCAGGGGCTGAAAAGAAGTAGGAACTTAGCAAGAGGTGAAGTGGACATTCATGTTGGCAATGGAGCAAGTGT

Reverse complement sequence

ACACTTGCTCCATTGCCAACATGAATGTCCACTTCACCTCTTGCTAAGTTCCTACTTCTTTTCAGCCCCTGCAAAGATTTGCATATATGAGCAACTGACC[C/T]
GGTATCAAATACCCAAGAATCAGTAGAGGAAGTAGCAAGATTAATTTCTATAACATTAATACCTGAGGTGGAACTCTTTCCATCCTACTGCTTCTGCTTG

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 85.90% 13.90% 0.21% 0.00% NA
All Indica  2759 78.40% 21.20% 0.36% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 45.60% 54.00% 0.43% 0.00% NA
Indica III  913 86.10% 13.40% 0.55% 0.00% NA
Indica Intermediate  786 73.90% 25.70% 0.38% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 76.70% 23.30% 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
vg1113429006 G -> A LOC_Os11g23750.1 intron_variant ; MODIFIER silent_mutation Average:25.757; most accessible tissue: Minghui63 panicle, score: 34.226 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1113429006 NA 3.06E-06 mr1343 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
vg1113429006 NA 4.13E-09 mr1829 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
vg1113429006 NA 3.69E-14 mr1829 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
vg1113429006 NA 1.47E-10 mr1842 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
vg1113429006 8.98E-06 NA mr1902 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
vg1113429006 8.39E-06 3.13E-12 mr1902 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
vg1113429006 NA 8.72E-11 mr1829_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
vg1113429006 NA 1.80E-06 mr1842_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
vg1113429006 NA 5.43E-10 mr1902_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
vg1113429006 NA 2.53E-07 mr1933_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