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Detailed information for vg0226052907:

Variant ID: vg0226052907 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26052907
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GGACGGAGTGAGTATTAAAGAAAGAACACAATATTTCACGGAAAGCACTTGGGACACGTGGCGTTGCTTTTCTGCGGGGCCCCACGGCAGAAGGAGAACT[G/T]
GTGTGGACACTTTGGCAAGCAATTGTCCGCCAAACTCACCACCGCGCCGTCCTCCTTCAGCTGCCTCAGCTGGCTCGGCAGGGCCCCACAGAGAAAGTTC

Reverse complement sequence

GAACTTTCTCTGTGGGGCCCTGCCGAGCCAGCTGAGGCAGCTGAAGGAGGACGGCGCGGTGGTGAGTTTGGCGGACAATTGCTTGCCAAAGTGTCCACAC[C/A]
AGTTCTCCTTCTGCCGTGGGGCCCCGCAGAAAAGCAACGCCACGTGTCCCAAGTGCTTTCCGTGAAATATTGTGTTCTTTCTTTAATACTCACTCCGTCC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.70% 30.20% 0.13% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 19.00% 80.60% 0.40% 0.00% NA
Aus  269 95.50% 4.50% 0.00% 0.00% NA
Indica I  595 98.50% 1.50% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 94.90% 5.10% 0.00% 0.00% NA
Temperate Japonica  767 6.10% 93.40% 0.52% 0.00% NA
Tropical Japonica  504 33.90% 65.90% 0.20% 0.00% NA
Japonica Intermediate  241 29.00% 70.50% 0.41% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 0.00% 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
vg0226052907 G -> T LOC_Os02g43250.1 missense_variant ; p.Gln420Lys; MODERATE nonsynonymous_codon ; Q420K Average:98.483; most accessible tissue: Zhenshan97 panicle, score: 99.663 possibly damaging -1.715 TOLERATED 1.00

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)
vg0226052907 G T -0.05 -0.05 0.0 -0.05 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226052907 NA 4.06E-13 mr1239 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
vg0226052907 NA 5.97E-13 mr1853 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
vg0226052907 NA 6.73E-15 mr1133_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
vg0226052907 NA 5.47E-11 mr1667_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