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Detailed information for vg0921852094:

Variant ID: vg0921852094 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21852094
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


GGAGCCGATGTCTTCCCCAGCCACCGCCGAAGCTGTGGTCTTCCCCATCCGGCGCCGCCGAACTCCACCGATGCCGCATGCCACCCTGCTGAGGACCTCC[G/A]
ACATCGTCATCGTCTCCTCCCCAACATGCACTCCTGCCTCCCCAGCCATCCCAGAACTGCCGCAGACCTTCGACACAAATGGCCTCAACCTCCTCCTGTT

Reverse complement sequence

AACAGGAGGAGGTTGAGGCCATTTGTGTCGAAGGTCTGCGGCAGTTCTGGGATGGCTGGGGAGGCAGGAGTGCATGTTGGGGAGGAGACGATGACGATGT[C/T]
GGAGGTCCTCAGCAGGGTGGCATGCGGCATCGGTGGAGTTCGGCGGCGCCGGATGGGGAAGACCACAGCTTCGGCGGTGGCTGGGGAAGACATCGGCTCC

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 41.20% 1.70% 0.78% 56.33% NA
All Indica  2759 8.30% 2.60% 1.12% 88.00% NA
All Japonica  1512 99.50% 0.10% 0.00% 0.40% NA
Aus  269 27.50% 1.90% 1.86% 68.77% NA
Indica I  595 1.80% 1.20% 1.34% 95.63% NA
Indica II  465 21.70% 3.70% 0.43% 74.19% NA
Indica III  913 6.50% 2.20% 1.31% 90.03% NA
Indica Intermediate  786 7.40% 3.40% 1.15% 88.04% NA
Temperate Japonica  767 99.70% 0.10% 0.00% 0.13% NA
Tropical Japonica  504 99.40% 0.00% 0.00% 0.60% NA
Japonica Intermediate  241 99.20% 0.00% 0.00% 0.83% NA
VI/Aromatic  96 85.40% 1.00% 0.00% 13.54% NA
Intermediate  90 65.60% 0.00% 1.11% 33.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0921852094 G -> DEL N N silent_mutation Average:56.567; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N
vg0921852094 G -> A LOC_Os09g37890.1 upstream_gene_variant ; 2076.0bp to feature; MODIFIER silent_mutation Average:56.567; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N
vg0921852094 G -> A LOC_Os09g37910.1 upstream_gene_variant ; 4778.0bp to feature; MODIFIER silent_mutation Average:56.567; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N
vg0921852094 G -> A LOC_Os09g37890-LOC_Os09g37910 intergenic_region ; MODIFIER silent_mutation Average:56.567; most accessible tissue: Minghui63 young leaf, score: 70.655 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921852094 5.35E-07 5.55E-72 mr1865 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
vg0921852094 NA 1.09E-14 mr1133_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
vg0921852094 NA 5.88E-16 mr1148_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
vg0921852094 NA 5.53E-13 mr1151_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
vg0921852094 NA 1.14E-12 mr1258_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
vg0921852094 NA 5.32E-10 mr1506_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
vg0921852094 NA 3.50E-21 mr1698_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
vg0921852094 NA 8.62E-13 mr1717_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
vg0921852094 NA 4.91E-11 mr1835_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
vg0921852094 NA 2.79E-18 mr1836_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
vg0921852094 2.56E-06 NA mr1865_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
vg0921852094 NA 2.96E-34 mr1873_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
vg0921852094 NA 4.78E-21 mr1922_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