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Detailed information for vg0920135790:

Variant ID: vg0920135790 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 20135790
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.64, G: 0.37, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:


GCCTTGTTTAGATCCTCCAAAATAGCAGCAAAAGTTTTGCTATTTTATAGCACTTTTTGCCATTTTGGATCTAAACACTAGTAGTAAAAGTTGGCAATTT[A/G]
GCATTTGCTAATCCATAGTAGCAAATTGTGCCAAAAAAGTGCTTTAGTACCACTCCCTCTCTCTTTCTCTCTCTCACTTTAGTGCTAGAATGGCAAAACT

Reverse complement sequence

AGTTTTGCCATTCTAGCACTAAAGTGAGAGAGAGAAAGAGAGAGGGAGTGGTACTAAAGCACTTTTTTGGCACAATTTGCTACTATGGATTAGCAAATGC[T/C]
AAATTGCCAACTTTTACTACTAGTGTTTAGATCCAAAATGGCAAAAAGTGCTATAAAATAGCAAAACTTTTGCTGCTATTTTGGAGGATCTAAACAAGGC

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 57.00% 38.60% 1.84% 2.54% NA
All Indica  2759 89.00% 4.40% 2.54% 4.02% NA
All Japonica  1512 0.50% 99.40% 0.07% 0.00% NA
Aus  269 71.00% 20.40% 5.58% 2.97% NA
Indica I  595 90.60% 4.50% 3.36% 1.51% NA
Indica II  465 90.50% 5.60% 1.94% 1.94% NA
Indica III  913 90.60% 1.20% 1.64% 6.57% NA
Indica Intermediate  786 85.10% 7.40% 3.31% 4.20% NA
Temperate Japonica  767 0.10% 99.90% 0.00% 0.00% NA
Tropical Japonica  504 0.20% 99.60% 0.20% 0.00% NA
Japonica Intermediate  241 2.50% 97.50% 0.00% 0.00% NA
VI/Aromatic  96 11.50% 87.50% 1.04% 0.00% NA
Intermediate  90 33.30% 65.60% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0920135790 A -> G LOC_Os09g34110.1 upstream_gene_variant ; 1432.0bp to feature; MODIFIER silent_mutation Average:44.856; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0920135790 A -> G LOC_Os09g34110.2 upstream_gene_variant ; 1339.0bp to feature; MODIFIER silent_mutation Average:44.856; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0920135790 A -> G LOC_Os09g34110-LOC_Os09g34120 intergenic_region ; MODIFIER silent_mutation Average:44.856; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N
vg0920135790 A -> DEL N N silent_mutation Average:44.856; most accessible tissue: Zhenshan97 panicle, score: 78.302 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0920135790 1.91E-08 NA mr1216 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
vg0920135790 NA 1.78E-09 mr1216 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
vg0920135790 NA 5.31E-16 mr1324 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
vg0920135790 NA 3.91E-11 mr1325 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
vg0920135790 NA 2.55E-13 mr1326 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
vg0920135790 NA 3.03E-13 mr1335 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
vg0920135790 NA 8.24E-08 mr1506 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
vg0920135790 NA 1.02E-20 mr1518 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
vg0920135790 3.78E-06 5.33E-10 mr1518 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
vg0920135790 NA 3.42E-11 mr1623 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
vg0920135790 NA 5.37E-09 mr1660 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
vg0920135790 NA 1.34E-21 mr1676 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
vg0920135790 4.82E-07 3.71E-12 mr1676 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
vg0920135790 NA 1.25E-06 mr1781 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
vg0920135790 NA 9.27E-58 mr1064_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
vg0920135790 NA 4.22E-06 mr1064_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
vg0920135790 1.64E-06 NA mr1216_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
vg0920135790 NA 1.00E-10 mr1349_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
vg0920135790 4.48E-06 2.37E-24 mr1676_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
vg0920135790 1.06E-10 3.77E-16 mr1676_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
vg0920135790 NA 6.71E-07 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