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Detailed information for vg1110542233:

Variant ID: vg1110542233 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 10542233
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: 85. )

Flanking Sequence (100 bp) in Reference Genome:


GCAACCTTATGAGTGTCGTAGGCTCTCCGGACCTTCCATTATATTTGAGAGATGAAATGAATAATTCAAGTCATCAAACAAGCATAATGAAACATCCAAC[G/A]
CCTCGAGAGAGGAATATTGGAGACATTGCTAGGCCCTTAGCCTGCCAGTCAACTTCAGCCTGAGATGTGCCCGTCAAACCACTCGAAGGCAGCGACCAGA

Reverse complement sequence

TCTGGTCGCTGCCTTCGAGTGGTTTGACGGGCACATCTCAGGCTGAAGTTGACTGGCAGGCTAAGGGCCTAGCAATGTCTCCAATATTCCTCTCTCGAGG[C/T]
GTTGGATGTTTCATTATGCTTGTTTGATGACTTGAATTATTCATTTCATCTCTCAAATATAATGGAAGGTCCGGAGAGCCTACGACACTCATAAGGTTGC

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 68.20% 30.10% 0.40% 1.31% NA
All Indica  2759 51.00% 47.90% 0.58% 0.58% NA
All Japonica  1512 98.60% 1.10% 0.13% 0.20% NA
Aus  269 83.60% 16.40% 0.00% 0.00% NA
Indica I  595 75.50% 24.00% 0.17% 0.34% NA
Indica II  465 17.40% 81.70% 0.65% 0.22% NA
Indica III  913 51.40% 47.40% 0.33% 0.88% NA
Indica Intermediate  786 51.80% 46.40% 1.15% 0.64% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 97.50% 0.80% 0.41% 1.24% NA
VI/Aromatic  96 52.10% 5.20% 0.00% 42.71% NA
Intermediate  90 55.60% 41.10% 1.11% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1110542233 G -> A LOC_Os11g18660.1 upstream_gene_variant ; 2878.0bp to feature; MODIFIER silent_mutation Average:38.247; most accessible tissue: Minghui63 young leaf, score: 51.901 N N N N
vg1110542233 G -> A LOC_Os11g18660-LOC_Os11g18670 intergenic_region ; MODIFIER silent_mutation Average:38.247; most accessible tissue: Minghui63 young leaf, score: 51.901 N N N N
vg1110542233 G -> DEL N N silent_mutation Average:38.247; most accessible tissue: Minghui63 young leaf, score: 51.901 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1110542233 NA 2.83E-08 mr1059 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
vg1110542233 NA 1.08E-09 mr1143 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
vg1110542233 NA 3.57E-09 mr1167 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
vg1110542233 NA 1.72E-06 mr1291 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
vg1110542233 NA 1.52E-06 mr1479 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
vg1110542233 NA 6.79E-07 mr1479 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
vg1110542233 NA 1.30E-06 mr1502 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
vg1110542233 NA 1.38E-08 mr1535 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
vg1110542233 NA 1.80E-09 mr1608 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
vg1110542233 NA 3.77E-09 mr1675 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
vg1110542233 NA 7.42E-08 mr1726 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
vg1110542233 NA 7.89E-06 mr1892 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
vg1110542233 NA 6.33E-06 mr1919 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
vg1110542233 NA 8.98E-08 mr1950 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