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Detailed information for vg0401680163:

Variant ID: vg0401680163 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1680163
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TGGTGGAGCAGCAGCTCAGCCGGATTCGCCTCGAGGCGACGGGAACAGCTGCGCGAACCCGCGGCTGCGCGTTGACGACGGTGTAGCCGCGCTCCAGAGC[T/C]
CCCGTGGCGAGGTCGGCGTTCCCAGAGATCGGCTGCAAGAAACGGGGCGAGATCAGAGAAGAGGCTATGGCGTGCAAGGGTGAATCGGGAACAGAAGAAA

Reverse complement sequence

TTTCTTCTGTTCCCGATTCACCCTTGCACGCCATAGCCTCTTCTCTGATCTCGCCCCGTTTCTTGCAGCCGATCTCTGGGAACGCCGACCTCGCCACGGG[A/G]
GCTCTGGAGCGCGGCTACACCGTCGTCAACGCGCAGCCGCGGGTTCGCGCAGCTGTTCCCGTCGCCTCGAGGCGAATCCGGCTGAGCTGCTGCTCCACCA

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 41.00% 37.20% 1.10% 20.74% NA
All Indica  2759 47.90% 30.00% 1.49% 20.66% NA
All Japonica  1512 19.60% 54.00% 0.33% 26.06% NA
Aus  269 85.90% 13.40% 0.74% 0.00% NA
Indica I  595 55.10% 34.50% 2.69% 7.73% NA
Indica II  465 34.40% 53.50% 0.65% 11.40% NA
Indica III  913 51.20% 8.90% 0.44% 39.54% NA
Indica Intermediate  786 46.60% 37.20% 2.29% 13.99% NA
Temperate Japonica  767 4.20% 84.10% 0.13% 11.60% NA
Tropical Japonica  504 46.60% 20.00% 0.79% 32.54% NA
Japonica Intermediate  241 12.00% 29.50% 0.00% 58.51% NA
VI/Aromatic  96 54.20% 36.50% 2.08% 7.29% NA
Intermediate  90 40.00% 47.80% 2.22% 10.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0401680163 T -> C LOC_Os04g03760.1 upstream_gene_variant ; 3318.0bp to feature; MODIFIER silent_mutation Average:50.258; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg0401680163 T -> C LOC_Os04g03760-LOC_Os04g03780 intergenic_region ; MODIFIER silent_mutation Average:50.258; most accessible tissue: Zhenshan97 panicle, score: 97.094 N N N N
vg0401680163 T -> DEL N N silent_mutation Average:50.258; most accessible tissue: Zhenshan97 panicle, score: 97.094 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)
vg0401680163 T C 0.01 0.0 0.01 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401680163 NA 3.36E-07 mr1829 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
vg0401680163 NA 1.97E-06 mr1553_2 Jap_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
vg0401680163 NA 8.74E-07 mr1705_2 Jap_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
vg0401680163 NA 1.74E-10 mr1817_2 Jap_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