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Detailed information for vg0916388935:

Variant ID: vg0916388935 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16388935
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:


TGTCACTGCATTTCTGCCCCCAAAAAATGTTTTCAGATCAACTTCAAATATCTACACGCTTCAATAAACTGGAAAATCACATACTAATACTGTAATTAAT[A/G]
GGAACAATCTTGAATGGGTGCAGTCACAAACTCTCAGAATGATAGCTGCAGGCTGCAACTATGTACTCGTAGCATTCTTGTTAGTCAACTTCTGAAACTT

Reverse complement sequence

AAGTTTCAGAAGTTGACTAACAAGAATGCTACGAGTACATAGTTGCAGCCTGCAGCTATCATTCTGAGAGTTTGTGACTGCACCCATTCAAGATTGTTCC[T/C]
ATTAATTACAGTATTAGTATGTGATTTTCCAGTTTATTGAAGCGTGTAGATATTTGAAGTTGATCTGAAAACATTTTTTGGGGGCAGAAATGCAGTGACA

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 72.60% 27.20% 0.13% 0.06% NA
All Indica  2759 53.90% 45.80% 0.22% 0.11% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 96.30% 3.70% 0.00% 0.00% NA
Indica II  465 24.90% 74.80% 0.22% 0.00% NA
Indica III  913 37.90% 62.00% 0.00% 0.11% NA
Indica Intermediate  786 57.40% 41.70% 0.64% 0.25% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 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
vg0916388935 A -> G LOC_Os09g26970.1 upstream_gene_variant ; 3935.0bp to feature; MODIFIER silent_mutation Average:88.485; most accessible tissue: Minghui63 flag leaf, score: 95.569 N N N N
vg0916388935 A -> G LOC_Os09g26960.1 intron_variant ; MODIFIER silent_mutation Average:88.485; most accessible tissue: Minghui63 flag leaf, score: 95.569 N N N N
vg0916388935 A -> DEL N N silent_mutation Average:88.485; most accessible tissue: Minghui63 flag leaf, score: 95.569 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)
vg0916388935 A G 0.04 0.03 0.01 0.02 0.03 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0916388935 NA 2.45E-10 mr1174 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
vg0916388935 NA 6.74E-06 mr1502 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
vg0916388935 NA 1.29E-06 mr1695 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
vg0916388935 NA 8.23E-08 mr1974 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
vg0916388935 NA 4.42E-07 mr1974 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
vg0916388935 NA 2.34E-07 mr1527_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
vg0916388935 NA 4.57E-09 mr1598_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
vg0916388935 NA 4.75E-08 mr1659_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
vg0916388935 NA 2.68E-07 mr1904_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