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Detailed information for vg0905794041:

Variant ID: vg0905794041 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 5794041
Reference Allele: TAlternative Allele: A
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, A: 0.16, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


TGGAGGAGCTCTGCCGACGCTGCGGGCGCTGATGTCGATGTTGATGTCGACGCCGCCCACCACGACATCATGCCGCTCCCGCCGTGGAGGCTGGAGGAGC[T/A]
ACACAGGGTCGTGGAGCTTGAGGAGAGGAAGGCCGTGGCTACCATGTGACTAGCTGAGGTGCGCGCCAGGAAGCGGGAGACCGCCGAGCAAGGGCGTGGC

Reverse complement sequence

GCCACGCCCTTGCTCGGCGGTCTCCCGCTTCCTGGCGCGCACCTCAGCTAGTCACATGGTAGCCACGGCCTTCCTCTCCTCAAGCTCCACGACCCTGTGT[A/T]
GCTCCTCCAGCCTCCACGGCGGGAGCGGCATGATGTCGTGGTGGGCGGCGTCGACATCAACATCGACATCAGCGCCCGCAGCGTCGGCAGAGCTCCTCCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.60% 43.30% 1.14% 0.00% NA
All Indica  2759 86.70% 13.20% 0.11% 0.00% NA
All Japonica  1512 8.50% 88.20% 3.31% 0.00% NA
Aus  269 23.00% 77.00% 0.00% 0.00% NA
Indica I  595 86.90% 13.10% 0.00% 0.00% NA
Indica II  465 84.90% 15.10% 0.00% 0.00% NA
Indica III  913 91.10% 8.80% 0.11% 0.00% NA
Indica Intermediate  786 82.30% 17.40% 0.25% 0.00% NA
Temperate Japonica  767 1.30% 96.30% 2.35% 0.00% NA
Tropical Japonica  504 14.30% 84.50% 1.19% 0.00% NA
Japonica Intermediate  241 19.50% 69.70% 10.79% 0.00% NA
VI/Aromatic  96 3.10% 96.90% 0.00% 0.00% NA
Intermediate  90 45.60% 53.30% 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
vg0905794041 T -> A LOC_Os09g10640.1 upstream_gene_variant ; 2916.0bp to feature; MODIFIER silent_mutation Average:84.56; most accessible tissue: Minghui63 flag leaf, score: 93.917 N N N N
vg0905794041 T -> A LOC_Os09g10620.1 downstream_gene_variant ; 3683.0bp to feature; MODIFIER silent_mutation Average:84.56; most accessible tissue: Minghui63 flag leaf, score: 93.917 N N N N
vg0905794041 T -> A LOC_Os09g10630.1 downstream_gene_variant ; 69.0bp to feature; MODIFIER silent_mutation Average:84.56; most accessible tissue: Minghui63 flag leaf, score: 93.917 N N N N
vg0905794041 T -> A LOC_Os09g10630-LOC_Os09g10640 intergenic_region ; MODIFIER silent_mutation Average:84.56; most accessible tissue: Minghui63 flag leaf, score: 93.917 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)
vg0905794041 T A -0.03 -0.03 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0905794041 5.74E-06 8.14E-08 mr1272 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