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Detailed information for vg0229381690:

Variant ID: vg0229381690 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 29381690
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.04, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAAGTGAGCACATGCTGCAAACAAACCGTCTCGAAAGAAAAAGAAAATATCACAACAGAACAGAACAGCATGCCTTAGGGACAAAGGCAAAGAGTCCA[G/A]
CATAGATATTCCTTAGCCGCGTAAGCCAGAAGACCGGCGATTGCTTGCATCGAAGCAGACGTCCATTGGAAGGCCCAGACAGCTGACGTATATACAAGCC

Reverse complement sequence

GGCTTGTATATACGTCAGCTGTCTGGGCCTTCCAATGGACGTCTGCTTCGATGCAAGCAATCGCCGGTCTTCTGGCTTACGCGGCTAAGGAATATCTATG[C/T]
TGGACTCTTTGCCTTTGTCCCTAAGGCATGCTGTTCTGTTCTGTTGTGATATTTTCTTTTTCTTTCGAGACGGTTTGTTTGCAGCATGTGCTCACTTTCA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.10% 36.80% 0.08% 0.00% NA
All Indica  2759 37.90% 61.90% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 97.80% 2.20% 0.00% 0.00% NA
Indica I  595 21.20% 78.50% 0.34% 0.00% NA
Indica II  465 46.70% 53.30% 0.00% 0.00% NA
Indica III  913 41.80% 58.10% 0.11% 0.00% NA
Indica Intermediate  786 40.80% 59.00% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 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
vg0229381690 G -> A LOC_Os02g48000.1 upstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:94.157; most accessible tissue: Callus, score: 99.704 N N N N
vg0229381690 G -> A LOC_Os02g48000.2 upstream_gene_variant ; 1087.0bp to feature; MODIFIER silent_mutation Average:94.157; most accessible tissue: Callus, score: 99.704 N N N N
vg0229381690 G -> A LOC_Os02g48000.3 upstream_gene_variant ; 599.0bp to feature; MODIFIER silent_mutation Average:94.157; most accessible tissue: Callus, score: 99.704 N N N N
vg0229381690 G -> A LOC_Os02g48010.1 downstream_gene_variant ; 686.0bp to feature; MODIFIER silent_mutation Average:94.157; most accessible tissue: Callus, score: 99.704 N N N N
vg0229381690 G -> A LOC_Os02g48000-LOC_Os02g48010 intergenic_region ; MODIFIER silent_mutation Average:94.157; most accessible tissue: Callus, score: 99.704 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)
vg0229381690 G A -0.09 -0.02 0.02 -0.06 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0229381690 NA 8.93E-07 mr1029 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
vg0229381690 NA 6.86E-06 mr1189 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
vg0229381690 NA 5.53E-07 mr1625 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
vg0229381690 NA 2.95E-08 mr1707 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
vg0229381690 NA 1.12E-06 mr1796 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
vg0229381690 NA 3.03E-06 mr1881 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
vg0229381690 1.54E-06 NA mr1156_2 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
vg0229381690 4.40E-06 1.21E-06 mr1156_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
vg0229381690 NA 1.29E-08 mr1172_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
vg0229381690 2.31E-06 2.10E-16 mr1514_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