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Detailed information for vg0915839955:

Variant ID: vg0915839955 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 15839955
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:


TGTTAGAAGATAAAATATGAATAGTACTTTATACATGACTTACCTTTTTAAAATTTTTTATAAATTTTTTAAATAAGACGGACGGTTAAACGTTAGATAC[G/A]
AAAACCCAGAAATTGAGTTTTTTTTGGACGGAGGGAGTATGTCATAACCTAGCTAGCTGGAGTATACCTAAATGATGGACGACGCACAGATATACTCTTG

Reverse complement sequence

CAAGAGTATATCTGTGCGTCGTCCATCATTTAGGTATACTCCAGCTAGCTAGGTTATGACATACTCCCTCCGTCCAAAAAAAACTCAATTTCTGGGTTTT[C/T]
GTATCTAACGTTTAACCGTCCGTCTTATTTAAAAAATTTATAAAAAATTTTAAAAAGGTAAGTCATGTATAAAGTACTATTCATATTTTATCTTCTAACA

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 62.20% 37.20% 0.30% 0.23% NA
All Indica  2759 39.10% 60.00% 0.51% 0.40% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 71.40% 28.60% 0.00% 0.00% NA
Indica I  595 6.40% 92.10% 0.84% 0.67% NA
Indica II  465 61.70% 36.80% 0.43% 1.08% NA
Indica III  913 44.80% 55.00% 0.22% 0.00% NA
Indica Intermediate  786 43.90% 55.20% 0.64% 0.25% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 80.00% 20.00% 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
vg0915839955 G -> DEL N N silent_mutation Average:76.912; most accessible tissue: Callus, score: 92.778 N N N N
vg0915839955 G -> A LOC_Os09g26220.1 downstream_gene_variant ; 3437.0bp to feature; MODIFIER silent_mutation Average:76.912; most accessible tissue: Callus, score: 92.778 N N N N
vg0915839955 G -> A LOC_Os09g26210-LOC_Os09g26220 intergenic_region ; MODIFIER silent_mutation Average:76.912; most accessible tissue: Callus, score: 92.778 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)
vg0915839955 G A -0.03 -0.03 -0.02 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0915839955 NA 6.06E-06 mr1532 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
vg0915839955 NA 4.61E-06 mr1707 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
vg0915839955 NA 5.23E-10 mr1728 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
vg0915839955 NA 4.38E-08 mr1728 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
vg0915839955 8.47E-06 7.71E-08 mr1744 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
vg0915839955 NA 1.11E-11 mr1728_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
vg0915839955 NA 9.91E-08 mr1728_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
vg0915839955 NA 4.74E-06 mr1860_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