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Detailed information for vg0105957608:

Variant ID: vg0105957608 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5957608
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.78, T: 0.22, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTCTAAGGGTGTGTTTGGATGGAGGGATATGGGTGGATAGGACATGGCCGCCTATTTTTTTTGTAGGTGTTTGGTTGCTGGGCAGGGGTGGGATGGGG[C/T]
GGCTCGGGGAGGAATATTCCCCCAGATGCTGGATGGGGGGATCCGGCCGATTTGCCCGGATCCAGCCGCCTGAGCGCCCGGGCGAGCGAGGGAGGGAGGC

Reverse complement sequence

GCCTCCCTCCCTCGCTCGCCCGGGCGCTCAGGCGGCTGGATCCGGGCAAATCGGCCGGATCCCCCCATCCAGCATCTGGGGGAATATTCCTCCCCGAGCC[G/A]
CCCCATCCCACCCCTGCCCAGCAACCAAACACCTACAAAAAAAATAGGCGGCCATGTCCTATCCACCCATATCCCTCCATCCAAACACACCCTTAGAGAA

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 65.20% 34.70% 0.08% 0.00% NA
All Indica  2759 62.10% 37.70% 0.14% 0.00% NA
All Japonica  1512 79.00% 21.00% 0.00% 0.00% NA
Aus  269 11.20% 88.80% 0.00% 0.00% NA
Indica I  595 91.10% 8.90% 0.00% 0.00% NA
Indica II  465 63.20% 36.80% 0.00% 0.00% NA
Indica III  913 45.50% 54.30% 0.22% 0.00% NA
Indica Intermediate  786 58.90% 40.80% 0.25% 0.00% NA
Temperate Japonica  767 95.70% 4.30% 0.00% 0.00% NA
Tropical Japonica  504 70.00% 30.00% 0.00% 0.00% NA
Japonica Intermediate  241 44.80% 55.20% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 71.10% 28.90% 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
vg0105957608 C -> T LOC_Os01g11130.1 upstream_gene_variant ; 3221.0bp to feature; MODIFIER silent_mutation Average:75.364; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0105957608 C -> T LOC_Os01g11140.1 upstream_gene_variant ; 4086.0bp to feature; MODIFIER silent_mutation Average:75.364; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 N N N N
vg0105957608 C -> T LOC_Os01g11130-LOC_Os01g11140 intergenic_region ; MODIFIER silent_mutation Average:75.364; most accessible tissue: Zhenshan97 flag leaf, score: 84.998 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)
vg0105957608 C T -0.02 -0.03 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105957608 NA 4.97E-06 mr1155_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
vg0105957608 3.27E-06 NA mr1728_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