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Detailed information for vg0916577384:

Variant ID: vg0916577384 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16577384
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


CAATAGACTAGATTAATAGTAAACCACATTAATAGTATGTCTACATGGGTATCTATAACTCTCTCATCCATTGCCTCGCTTTTCTCTATAGACTATCTAC[G/A]
GGTTAGTAGATAGCTTTACTCTCTCTCTTCATTTAATCTCTTTCAAGTAGTAAAATATGCTGACATGGATATCTTATAGAGAGCCTATAGATAACTATTG

Reverse complement sequence

CAATAGTTATCTATAGGCTCTCTATAAGATATCCATGTCAGCATATTTTACTACTTGAAAGAGATTAAATGAAGAGAGAGAGTAAAGCTATCTACTAACC[C/T]
GTAGATAGTCTATAGAGAAAAGCGAGGCAATGGATGAGAGAGTTATAGATACCCATGTAGACATACTATTAATGTGGTTTACTATTAATCTAGTCTATTG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 89.00% 10.50% 0.57% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 67.10% 31.20% 1.72% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.70% 0.30% 0.00% 0.00% NA
Temperate Japonica  767 46.90% 49.90% 3.13% 0.00% NA
Tropical Japonica  504 96.20% 3.80% 0.00% 0.00% NA
Japonica Intermediate  241 70.10% 29.00% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 82.20% 16.70% 1.11% 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
vg0916577384 G -> A LOC_Os09g27260.1 upstream_gene_variant ; 2491.0bp to feature; MODIFIER silent_mutation Average:77.643; most accessible tissue: Minghui63 panicle, score: 96.207 N N N N
vg0916577384 G -> A LOC_Os09g27270.1 downstream_gene_variant ; 3032.0bp to feature; MODIFIER silent_mutation Average:77.643; most accessible tissue: Minghui63 panicle, score: 96.207 N N N N
vg0916577384 G -> A LOC_Os09g27260-LOC_Os09g27270 intergenic_region ; MODIFIER silent_mutation Average:77.643; most accessible tissue: Minghui63 panicle, score: 96.207 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)
vg0916577384 G A 0.02 0.08 0.07 0.02 0.06 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916577384 NA 1.51E-06 mr1070 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
vg0916577384 2.26E-06 2.26E-06 mr1074 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
vg0916577384 NA 1.32E-07 mr1097 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
vg0916577384 NA 3.08E-06 mr1148 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
vg0916577384 NA 2.60E-06 mr1154 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
vg0916577384 7.23E-07 7.22E-07 mr1494 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
vg0916577384 4.79E-06 4.79E-06 mr1824 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