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Detailed information for vg0425192447:

Variant ID: vg0425192447 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 25192447
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.60, T: 0.40, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGAGGACGCGCTCGGCGGCCGGGAAGAGCACCGCGGCGACGTCCTGGACGACGAGGAGCTGCCTGTCCGCGAAGGCGAGCGCCGAGAGGCACCTCAGC[C/T]
GCAGCGGGCTCAGCACCGGGGCCGCCGCGCGGGAGGCGCCCCTGGCCACGCACCCCACCGGGCACCGCATCGCCTCCACGCGCCGGTACGCCCCGCGCGC

Reverse complement sequence

GCGCGCGGGGCGTACCGGCGCGTGGAGGCGATGCGGTGCCCGGTGGGGTGCGTGGCCAGGGGCGCCTCCCGCGCGGCGGCCCCGGTGCTGAGCCCGCTGC[G/A]
GCTGAGGTGCCTCTCGGCGCTCGCCTTCGCGGACAGGCAGCTCCTCGTCGTCCAGGACGTCGCCGCGGTGCTCTTCCCGGCCGCCGAGCGCGTCCTCGGC

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 58.40% 40.90% 0.66% 0.00% NA
All Indica  2759 35.00% 64.10% 0.87% 0.00% NA
All Japonica  1512 99.10% 0.80% 0.13% 0.00% NA
Aus  269 53.20% 46.50% 0.37% 0.00% NA
Indica I  595 19.70% 79.70% 0.67% 0.00% NA
Indica II  465 9.50% 89.20% 1.29% 0.00% NA
Indica III  913 53.10% 46.50% 0.33% 0.00% NA
Indica Intermediate  786 40.80% 57.80% 1.40% 0.00% NA
Temperate Japonica  767 99.60% 0.30% 0.13% 0.00% NA
Tropical Japonica  504 98.20% 1.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 63.30% 32.20% 4.44% 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
vg0425192447 C -> T LOC_Os04g42590.1 missense_variant ; p.Arg77Gln; MODERATE nonsynonymous_codon ; R77Q Average:92.642; most accessible tissue: Minghui63 flag leaf, score: 98.078 unknown unknown DELETERIOUS 0.00

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)
vg0425192447 C T -0.01 -0.01 -0.03 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0425192447 NA 1.31E-07 mr1798 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
vg0425192447 NA 3.92E-06 mr1672_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
vg0425192447 NA 4.03E-06 mr1870_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