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Detailed information for vg1120554158:

Variant ID: vg1120554158 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20554158
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.53, A: 0.47, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CTTCTTCTTCTTCTTTTTTTCTTCTTTCGAATGGCTAATGGATTGTTTGCGACAATTATTCGAGGGTAGAAGTAAATAGATTAACTATTATATAACTAAA[A/T]
ACACAATTTAAAACAATGATCTAAAATTTCATATATAAAAATATTTTGAAAGAAAAATCATATTGACTAGTAGTTTGGAAACATTTCTGACCTCCACTTA

Reverse complement sequence

TAAGTGGAGGTCAGAAATGTTTCCAAACTACTAGTCAATATGATTTTTCTTTCAAAATATTTTTATATATGAAATTTTAGATCATTGTTTTAAATTGTGT[T/A]
TTTAGTTATATAATAGTTAATCTATTTACTTCTACCCTCGAATAATTGTCGCAAACAATCCATTAGCCATTCGAAAGAAGAAAAAAAGAAGAAGAAGAAG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 65.40% 34.40% 0.19% 0.00% NA
All Indica  2759 75.00% 24.90% 0.14% 0.00% NA
All Japonica  1512 56.90% 43.00% 0.13% 0.00% NA
Aus  269 4.50% 95.20% 0.37% 0.00% NA
Indica I  595 71.40% 28.40% 0.17% 0.00% NA
Indica II  465 73.30% 26.70% 0.00% 0.00% NA
Indica III  913 79.40% 20.50% 0.11% 0.00% NA
Indica Intermediate  786 73.50% 26.20% 0.25% 0.00% NA
Temperate Japonica  767 32.70% 67.10% 0.13% 0.00% NA
Tropical Japonica  504 84.30% 15.50% 0.20% 0.00% NA
Japonica Intermediate  241 76.30% 23.70% 0.00% 0.00% NA
VI/Aromatic  96 89.60% 10.40% 0.00% 0.00% NA
Intermediate  90 68.90% 28.90% 2.22% 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
vg1120554158 A -> T LOC_Os11g35060-LOC_Os11g35070 intergenic_region ; MODIFIER silent_mutation Average:75.987; most accessible tissue: Minghui63 root, score: 95.775 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)
vg1120554158 A T 0.03 0.0 0.0 0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120554158 NA 2.44E-09 mr1137 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
vg1120554158 NA 5.01E-07 mr1521 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
vg1120554158 NA 3.33E-06 mr1596 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
vg1120554158 NA 1.28E-08 mr1617 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
vg1120554158 NA 9.86E-07 mr1763 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
vg1120554158 NA 2.15E-06 mr1389_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
vg1120554158 NA 4.57E-06 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
vg1120554158 4.77E-06 4.76E-06 mr1609_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
vg1120554158 NA 4.54E-06 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