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Detailed information for vg0901841716:

Variant ID: vg0901841716 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 1841716
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, C: 0.09, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GGTGTCCGCGGTCCCGGTTTGGCCGGCCTCCGGCCACCCCGACCTTTCAGGCTTAGATCCCCGGGGAGACTCACTGTCGAGCCCCCTCGGGAGGGGATTT[C/T]
GCTGCAATAAAATCCCAGGGGCGCCTGTTAAAAAAAACATAGAGAGAAAGGCAAAGCTAGAGTGAAGAGAGATAACGGAATCGGAAGGCGGCAGATGTAC

Reverse complement sequence

GTACATCTGCCGCCTTCCGATTCCGTTATCTCTCTTCACTCTAGCTTTGCCTTTCTCTCTATGTTTTTTTTAACAGGCGCCCCTGGGATTTTATTGCAGC[G/A]
AAATCCCCTCCCGAGGGGGCTCGACAGTGAGTCTCCCCGGGGATCTAAGCCTGAAAGGTCGGGGTGGCCGGAGGCCGGCCAAACCGGGACCGCGGACACC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 66.90% 32.90% 0.19% 0.00% NA
All Indica  2759 69.00% 30.70% 0.29% 0.00% NA
All Japonica  1512 65.00% 34.90% 0.07% 0.00% NA
Aus  269 81.80% 18.20% 0.00% 0.00% NA
Indica I  595 65.40% 33.80% 0.84% 0.00% NA
Indica II  465 65.80% 34.00% 0.22% 0.00% NA
Indica III  913 82.30% 17.60% 0.11% 0.00% NA
Indica Intermediate  786 58.40% 41.50% 0.13% 0.00% NA
Temperate Japonica  767 97.10% 2.90% 0.00% 0.00% NA
Tropical Japonica  504 22.40% 77.60% 0.00% 0.00% NA
Japonica Intermediate  241 51.90% 47.70% 0.41% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 54.40% 45.60% 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
vg0901841716 C -> T LOC_Os09g03660.1 missense_variant ; p.Glu352Lys; MODERATE nonsynonymous_codon ; E352K Average:74.071; most accessible tissue: Zhenshan97 flag leaf, score: 87.661 unknown unknown DELETERIOUS 0.03

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)
vg0901841716 C 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
vg0901841716 NA 3.16E-14 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901841716 NA 1.69E-12 Grain_width Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0901841716 6.13E-07 NA mr1208 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
vg0901841716 NA 6.56E-06 mr1295 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
vg0901841716 NA 2.04E-07 mr1125_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
vg0901841716 9.37E-09 NA mr1208_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
vg0901841716 NA 2.11E-07 mr1208_2 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
vg0901841716 NA 1.49E-10 mr1552_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
vg0901841716 NA 4.46E-08 mr1578_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