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Detailed information for vg1125582889:

Variant ID: vg1125582889 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25582889
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.09, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


TTTATTTTAATTGATATTTTAGACAATCACACGGTCTATAAGATTTATCTTTGATCTTATTTTTCTATTATAATATATACAATAAATAAATACATGTTTA[T/C]
TTTTATTATAGTATTTTGAAAGACAAATTTATATATGTTGTTTTAGTTTCTTTAAACTAAATATTTTTAAAGTCATAGATGATCAAAGTTATAAAAGTTT

Reverse complement sequence

AAACTTTTATAACTTTGATCATCTATGACTTTAAAAATATTTAGTTTAAAGAAACTAAAACAACATATATAAATTTGTCTTTCAAAATACTATAATAAAA[A/G]
TAAACATGTATTTATTTATTGTATATATTATAATAGAAAAATAAGATCAAAGATAAATCTTATAGACCGTGTGATTGTCTAAAATATCAATTAAAATAAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.40% 38.30% 5.92% 4.36% NA
All Indica  2759 31.80% 53.20% 7.97% 7.03% NA
All Japonica  1512 90.00% 9.30% 0.46% 0.20% NA
Aus  269 38.30% 44.20% 15.99% 1.49% NA
Indica I  595 50.90% 42.40% 4.71% 2.02% NA
Indica II  465 59.40% 35.30% 3.44% 1.94% NA
Indica III  913 5.60% 73.30% 8.76% 12.38% NA
Indica Intermediate  786 31.40% 48.70% 12.21% 7.63% NA
Temperate Japonica  767 92.30% 7.00% 0.39% 0.26% NA
Tropical Japonica  504 87.70% 11.90% 0.20% 0.20% NA
Japonica Intermediate  241 87.60% 11.20% 1.24% 0.00% NA
VI/Aromatic  96 44.80% 53.10% 2.08% 0.00% NA
Intermediate  90 51.10% 34.40% 8.89% 5.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1125582889 T -> DEL N N silent_mutation Average:54.636; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1125582889 T -> C LOC_Os11g42470.1 downstream_gene_variant ; 120.0bp to feature; MODIFIER silent_mutation Average:54.636; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1125582889 T -> C LOC_Os11g42480.1 downstream_gene_variant ; 1075.0bp to feature; MODIFIER silent_mutation Average:54.636; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N
vg1125582889 T -> C LOC_Os11g42470-LOC_Os11g42480 intergenic_region ; MODIFIER silent_mutation Average:54.636; most accessible tissue: Zhenshan97 flag leaf, score: 85.514 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg1125582889 T C -0.01 -0.01 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125582889 1.01E-08 6.92E-15 mr1133 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
vg1125582889 1.97E-20 1.78E-32 mr1191 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
vg1125582889 2.18E-18 2.03E-21 mr1191 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
vg1125582889 NA 9.83E-07 mr1380 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
vg1125582889 NA 1.31E-08 mr1561 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
vg1125582889 NA 7.09E-07 mr1561 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
vg1125582889 1.52E-27 3.06E-43 mr1644 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
vg1125582889 2.26E-26 8.09E-31 mr1644 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
vg1125582889 NA 1.46E-08 mr1667 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
vg1125582889 NA 5.80E-09 mr1908 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
vg1125582889 NA 1.84E-06 mr1908 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
vg1125582889 NA 2.63E-10 mr1133_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
vg1125582889 1.01E-24 1.82E-46 mr1191_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
vg1125582889 1.52E-24 1.59E-30 mr1191_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
vg1125582889 NA 1.91E-10 mr1380_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
vg1125582889 NA 9.66E-09 mr1380_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
vg1125582889 NA 8.17E-11 mr1561_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
vg1125582889 NA 6.79E-08 mr1561_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
vg1125582889 NA 4.16E-07 mr1667_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
vg1125582889 NA 7.22E-10 mr1875_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
vg1125582889 NA 1.18E-06 mr1875_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
vg1125582889 6.76E-06 NA mr1900_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
vg1125582889 NA 2.66E-10 mr1908_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
vg1125582889 NA 1.85E-06 mr1908_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
vg1125582889 NA 4.73E-09 mr1996_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
vg1125582889 NA 1.51E-07 mr1996_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