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Detailed information for vg0108993891:

Variant ID: vg0108993891 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 8993891
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.74, A: 0.26, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:


TATTTTTAAGACAAATCCATTCATATAATTTTTATATTTTCAAACTCAACAACTTGAGAGTTATTCATGATTTATATTTTCAATGTTTGACTTAAACATT[A/G]
TCCTAAACGACTTACTTTACGAGTATGAAGGGAATATGTGTTAAGCGAGTGTACTCGTAAGCATATGTGCTCGTCTGAATTGAAAAATTAAAAATCTGTC

Reverse complement sequence

GACAGATTTTTAATTTTTCAATTCAGACGAGCACATATGCTTACGAGTACACTCGCTTAACACATATTCCCTTCATACTCGTAAAGTAAGTCGTTTAGGA[T/C]
AATGTTTAAGTCAAACATTGAAAATATAAATCATGAATAACTCTCAAGTTGTTGAGTTTGAAAATATAAAAATTATATGAATGGATTTGTCTTAAAAATA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.30% 41.00% 2.45% 1.18% NA
All Indica  2759 35.30% 61.30% 2.32% 1.05% NA
All Japonica  1512 97.60% 2.30% 0.07% 0.00% NA
Aus  269 4.10% 66.90% 18.96% 10.04% NA
Indica I  595 48.70% 50.60% 0.67% 0.00% NA
Indica II  465 52.30% 44.90% 2.37% 0.43% NA
Indica III  913 20.00% 76.20% 2.30% 1.42% NA
Indica Intermediate  786 32.80% 61.80% 3.56% 1.78% NA
Temperate Japonica  767 99.50% 0.50% 0.00% 0.00% NA
Tropical Japonica  504 94.60% 5.20% 0.20% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 66.70% 33.30% 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
vg0108993891 A -> G LOC_Os01g15990.1 upstream_gene_variant ; 1086.0bp to feature; MODIFIER silent_mutation Average:54.801; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0108993891 A -> G LOC_Os01g15979.1 downstream_gene_variant ; 1310.0bp to feature; MODIFIER silent_mutation Average:54.801; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0108993891 A -> G LOC_Os01g15979-LOC_Os01g15990 intergenic_region ; MODIFIER silent_mutation Average:54.801; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N
vg0108993891 A -> DEL N N silent_mutation Average:54.801; most accessible tissue: Minghui63 panicle, score: 78.92 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0108993891 NA 6.66E-06 mr1004 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
vg0108993891 NA 1.33E-08 mr1005 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
vg0108993891 NA 6.95E-13 mr1188 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
vg0108993891 NA 9.38E-10 mr1188 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
vg0108993891 NA 1.53E-09 mr1322 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
vg0108993891 NA 7.95E-07 mr1677 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
vg0108993891 NA 1.44E-06 mr1175_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
vg0108993891 NA 5.06E-06 mr1188_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
vg0108993891 NA 9.57E-12 mr1193_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
vg0108993891 NA 6.12E-06 mr1268_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
vg0108993891 NA 2.42E-06 mr1968_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
vg0108993891 NA 3.97E-06 mr1970_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
vg0108993891 NA 2.72E-06 mr1974_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