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Detailed information for vg1127143286:

Variant ID: vg1127143286 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27143286
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 127. )

Flanking Sequence (100 bp) in Reference Genome:


GGGGAGGCTAATGGGCGATCGATCGCCAGGGCGATCGCCCAGCGATCGGTTTGCCCCCCTCTCCCCCTATACTCCTCCCTTTTCTCTCCCTTCCTCCTCC[C/T]
CTTCTTCTCTTTCTACTACAGTACACCACACAAATTTTTTTTAAAAAACAAAAGTTAGAAAAATTTATGTATAGAAATACTATATATAAAAAATTTGAAT

Reverse complement sequence

ATTCAAATTTTTTATATATAGTATTTCTATACATAAATTTTTCTAACTTTTGTTTTTTAAAAAAAATTTGTGTGGTGTACTGTAGTAGAAAGAGAAGAAG[G/A]
GGAGGAGGAAGGGAGAGAAAAGGGAGGAGTATAGGGGGAGAGGGGGGCAAACCGATCGCTGGGCGATCGCCCTGGCGATCGATCGCCCATTAGCCTCCCC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.20% 3.90% 2.03% 3.85% NA
All Indica  2759 85.40% 6.50% 3.15% 4.93% NA
All Japonica  1512 99.30% 0.20% 0.13% 0.40% NA
Aus  269 98.90% 0.00% 0.00% 1.12% NA
Indica I  595 91.10% 1.50% 0.34% 7.06% NA
Indica II  465 64.70% 24.10% 10.97% 0.22% NA
Indica III  913 93.40% 0.10% 1.31% 5.15% NA
Indica Intermediate  786 84.10% 7.30% 2.80% 5.85% NA
Temperate Japonica  767 99.60% 0.00% 0.26% 0.13% NA
Tropical Japonica  504 99.00% 0.40% 0.00% 0.60% NA
Japonica Intermediate  241 98.80% 0.40% 0.00% 0.83% NA
VI/Aromatic  96 60.40% 0.00% 5.21% 34.38% NA
Intermediate  90 90.00% 3.30% 2.22% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1127143286 C -> T LOC_Os11g44840.1 upstream_gene_variant ; 2450.0bp to feature; MODIFIER silent_mutation Average:61.397; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N
vg1127143286 C -> T LOC_Os11g44850.1 upstream_gene_variant ; 1294.0bp to feature; MODIFIER silent_mutation Average:61.397; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N
vg1127143286 C -> T LOC_Os11g44840-LOC_Os11g44850 intergenic_region ; MODIFIER silent_mutation Average:61.397; most accessible tissue: Minghui63 young leaf, score: 75.479 N N N N
vg1127143286 C -> DEL N N silent_mutation Average:61.397; most accessible tissue: Minghui63 young leaf, score: 75.479 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)
vg1127143286 C T -0.01 -0.02 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127143286 NA 1.93E-07 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
vg1127143286 NA 4.20E-07 mr1498 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
vg1127143286 NA 7.97E-07 mr1951 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
vg1127143286 NA 4.94E-06 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
vg1127143286 NA 1.48E-08 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
vg1127143286 NA 2.13E-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
vg1127143286 NA 6.20E-08 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
vg1127143286 NA 3.04E-09 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
vg1127143286 NA 2.28E-07 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
vg1127143286 NA 3.11E-10 mr1875_2 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
vg1127143286 NA 3.02E-07 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
vg1127143286 NA 2.74E-09 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
vg1127143286 NA 4.24E-06 mr1931_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
vg1127143286 NA 1.76E-06 mr1931_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
vg1127143286 NA 2.21E-07 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
vg1127143286 NA 3.37E-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