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Detailed information for vg0224767711:

Variant ID: vg0224767711 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24767711
Reference Allele: GAlternative Allele: T
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.06, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTTACGCCAATGTATATATTGTAGTAATTAGTATTGCATTGGTTTCTTTTGTGCTGATGTTGTGATGCGAATATGGTTTGTTCTGCCCTCCTAGAAAA[G/T]
ATTAGATCACCTGAGGTGTAACAGAGTTTGCATTGCTGCATGATCAGAAATTTGAATGAAGCTACATGTATACGTCCTTGTGAAATCGTTGACATGACCT

Reverse complement sequence

AGGTCATGTCAACGATTTCACAAGGACGTATACATGTAGCTTCATTCAAATTTCTGATCATGCAGCAATGCAAACTCTGTTACACCTCAGGTGATCTAAT[C/A]
TTTTCTAGGAGGGCAGAACAAACCATATTCGCATCACAACATCAGCACAAAAGAAACCAATGCAATACTAATTACTACAATATATACATTGGCGTAAGAA

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 66.20% 33.70% 0.15% 0.00% NA
All Indica  2759 90.50% 9.20% 0.22% 0.00% NA
All Japonica  1512 22.00% 78.00% 0.00% 0.00% NA
Aus  269 87.40% 12.60% 0.00% 0.00% NA
Indica I  595 98.30% 1.70% 0.00% 0.00% NA
Indica II  465 94.60% 4.50% 0.86% 0.00% NA
Indica III  913 87.70% 12.30% 0.00% 0.00% NA
Indica Intermediate  786 85.50% 14.20% 0.25% 0.00% NA
Temperate Japonica  767 13.70% 86.30% 0.00% 0.00% NA
Tropical Japonica  504 30.80% 69.20% 0.00% 0.00% NA
Japonica Intermediate  241 30.30% 69.70% 0.00% 0.00% NA
VI/Aromatic  96 16.70% 83.30% 0.00% 0.00% NA
Intermediate  90 51.10% 47.80% 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
vg0224767711 G -> T LOC_Os02g40850.1 upstream_gene_variant ; 2419.0bp to feature; MODIFIER silent_mutation Average:76.069; most accessible tissue: Callus, score: 90.819 N N N N
vg0224767711 G -> T LOC_Os02g40860.1 intron_variant ; MODIFIER silent_mutation Average:76.069; most accessible tissue: Callus, score: 90.819 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)
vg0224767711 G T -0.01 -0.01 -0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224767711 NA 5.77E-11 mr1893_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
vg0224767711 8.63E-07 NA mr1929_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
vg0224767711 NA 4.44E-07 mr1929_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