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Detailed information for vg0913674199:

Variant ID: vg0913674199 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 13674199
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.92, T: 0.09, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCGCCTCCTGACTGACGCAGGGAGCGTCGAGCTGAATGTCCCCGCTCCCCGCATCACAGGCGTCCCATCGATCTTCGCGAAACTATCAACCAGCGCCG[T/C]
GCGGCGAGAGGCTACATCCCCCACCATTCACCAGATCGCTATAACGACGACGTGGATGGAGTTGCTGCCTTCACAAGCGACCTGCGTCGAGTGGATTGGC

Reverse complement sequence

GCCAATCCACTCGACGCAGGTCGCTTGTGAAGGCAGCAACTCCATCCACGTCGTCGTTATAGCGATCTGGTGAATGGTGGGGGATGTAGCCTCTCGCCGC[A/G]
CGGCGCTGGTTGATAGTTTCGCGAAGATCGATGGGACGCCTGTGATGCGGGGAGCGGGGACATTCAGCTCGACGCTCCCTGCGTCAGTCAGGAGGCGAGT

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 58.40% 36.70% 0.55% 4.36% NA
All Indica  2759 83.20% 9.60% 0.69% 6.45% NA
All Japonica  1512 9.90% 89.90% 0.26% 0.00% NA
Aus  269 88.50% 1.50% 0.37% 9.67% NA
Indica I  595 83.00% 0.80% 1.85% 14.29% NA
Indica II  465 94.40% 3.00% 0.22% 2.37% NA
Indica III  913 75.60% 19.90% 0.33% 4.16% NA
Indica Intermediate  786 85.60% 8.30% 0.51% 5.60% NA
Temperate Japonica  767 5.60% 94.10% 0.26% 0.00% NA
Tropical Japonica  504 17.50% 82.10% 0.40% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 44.40% 51.10% 2.22% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0913674199 T -> DEL LOC_Os09g23120.1 N frameshift_variant Average:68.409; most accessible tissue: Zhenshan97 flag leaf, score: 85.13 N N N N
vg0913674199 T -> C LOC_Os09g23120.1 synonymous_variant ; p.Arg291Arg; LOW synonymous_codon Average:68.409; most accessible tissue: Zhenshan97 flag leaf, score: 85.13 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)
vg0913674199 T C 0.0 0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0913674199 NA 3.74E-09 mr1198 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
vg0913674199 3.67E-07 3.67E-07 mr1260 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
vg0913674199 NA 6.18E-10 mr1307 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
vg0913674199 NA 3.64E-06 mr1508 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
vg0913674199 NA 2.94E-09 mr1986 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
vg0913674199 NA 7.17E-06 mr1913_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