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Detailed information for vg0921099453:

Variant ID: vg0921099453 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 21099453
Reference Allele: AAlternative Allele: C,T
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.73, A: 0.27, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


CCGGCAATCCCAACAGGTTGGCCAACTCTTTTTTTTTTTTTACAATTTTTACCTCTTCGCTTTACTTTGCGTGTGCATTGTCGTGCTCTGCCTATGTCCC[A/C,T]
AAAAAAAACTCAACCTACGATATACTCTATGAATCTGGACATAGAGTATATCTAGATTTATCGTATTAGGATGTGTCAGGTTAAGTTTTTCTGGGACGGA

Reverse complement sequence

TCCGTCCCAGAAAAACTTAACCTGACACATCCTAATACGATAAATCTAGATATACTCTATGTCCAGATTCATAGAGTATATCGTAGGTTGAGTTTTTTTT[T/G,A]
GGGACATAGGCAGAGCACGACAATGCACACGCAAAGTAAAGCGAAGAGGTAAAAATTGTAAAAAAAAAAAAAGAGTTGGCCAACCTGTTGGGATTGCCGG

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.00% 3.90% 0.08% 0.00% T: 0.02%
All Indica  2759 99.70% 0.20% 0.00% 0.00% T: 0.04%
All Japonica  1512 91.50% 8.20% 0.26% 0.00% NA
Aus  269 85.90% 14.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.00% 0.00% T: 0.11%
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 98.80% 1.00% 0.13% 0.00% NA
Tropical Japonica  504 77.20% 22.40% 0.40% 0.00% NA
Japonica Intermediate  241 98.30% 1.20% 0.41% 0.00% NA
VI/Aromatic  96 85.40% 14.60% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0921099453 A -> T LOC_Os09g36580.1 intron_variant ; MODIFIER silent_mutation Average:84.371; most accessible tissue: Zhenshan97 panicle, score: 94.949 N N N N
vg0921099453 A -> C LOC_Os09g36580.1 intron_variant ; MODIFIER silent_mutation Average:84.371; most accessible tissue: Zhenshan97 panicle, score: 94.949 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)
vg0921099453 A C -0.02 -0.01 0.01 -0.03 -0.02 -0.02
vg0921099453 A T 0.0 -0.01 -0.02 0.0 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0921099453 NA 4.27E-07 mr1045_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
vg0921099453 NA 1.51E-06 mr1097_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
vg0921099453 NA 3.83E-07 mr1204_2 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
vg0921099453 NA 8.73E-06 mr1220_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
vg0921099453 NA 4.32E-07 mr1252_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
vg0921099453 1.72E-06 8.24E-06 mr1298_2 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
vg0921099453 NA 1.17E-06 mr1405_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
vg0921099453 NA 1.20E-06 mr1567_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
vg0921099453 2.60E-06 NA mr1731_2 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
vg0921099453 6.67E-06 NA mr1735_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
vg0921099453 NA 8.22E-06 mr1740_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
vg0921099453 NA 4.66E-06 mr1844_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
vg0921099453 NA 4.19E-06 mr1887_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