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Detailed information for vg0527910633:

Variant ID: vg0527910633 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27910633
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TCCGTCCCAAAATAAGTACAGTTTTGCACTATTCACGTTCAACGTTTGACCGTTCGTCTTATTTGAATTTTTTTTATGATTAGTATTTTTATTGCTATTA[G/A]
ATGATAAAATATAAATAGTACCTATATGTGTGACTAAATATTTTTAAATTTTTTATAAATTTTTTAAATAAGACGAACGGTCAAACGTTGGGCACAGATA

Reverse complement sequence

TATCTGTGCCCAACGTTTGACCGTTCGTCTTATTTAAAAAATTTATAAAAAATTTAAAAATATTTAGTCACACATATAGGTACTATTTATATTTTATCAT[C/T]
TAATAGCAATAAAAATACTAATCATAAAAAAAATTCAAATAAGACGAACGGTCAAACGTTGAACGTGAATAGTGCAAAACTGTACTTATTTTGGGACGGA

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 75.60% 24.40% 0.08% 0.00% NA
All Indica  2759 77.00% 23.00% 0.04% 0.00% NA
All Japonica  1512 68.30% 31.70% 0.07% 0.00% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 91.40% 8.60% 0.00% 0.00% NA
Indica II  465 68.80% 31.20% 0.00% 0.00% NA
Indica III  913 67.10% 32.70% 0.11% 0.00% NA
Indica Intermediate  786 82.30% 17.70% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 13.10% 86.70% 0.20% 0.00% NA
Japonica Intermediate  241 86.70% 13.30% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 6.20% 1.04% 0.00% NA
Intermediate  90 72.20% 26.70% 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
vg0527910633 G -> A LOC_Os05g48700.1 downstream_gene_variant ; 98.0bp to feature; MODIFIER silent_mutation Average:61.617; most accessible tissue: Minghui63 panicle, score: 98.103 N N N N
vg0527910633 G -> A LOC_Os05g48690-LOC_Os05g48700 intergenic_region ; MODIFIER silent_mutation Average:61.617; most accessible tissue: Minghui63 panicle, score: 98.103 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)
vg0527910633 G A 0.0 0.01 0.0 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527910633 NA 4.74E-16 mr1115 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
vg0527910633 NA 3.91E-08 mr1194 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
vg0527910633 1.37E-06 2.78E-07 mr1701 Ind_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
vg0527910633 NA 8.70E-10 mr1347_2 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
vg0527910633 NA 1.74E-07 mr1551_2 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
vg0527910633 NA 3.76E-07 mr1696_2 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
vg0527910633 NA 1.58E-06 mr1860_2 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
vg0527910633 NA 2.03E-08 mr1879_2 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