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Detailed information for vg0502657346:

Variant ID: vg0502657346 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2657346
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 104. )

Flanking Sequence (100 bp) in Reference Genome:


GGAAAGTGGAGGCAATGGAGTAGTACTCGATGTCTCAATGCCTTTTCGTGGGGGTCCACCGGCTGTGGGCTTAGTATCCTAACTATAGGTGCTTGCACTG[C/T]
GAGATAAGTGTTTTTATCAAGTTTTGAGGCTGAGGTACGGGCCCTATAGCTTACATTGTAAATAGCCTGATAAGTAGTACTTGAGGTTAAACTGTGGCAC

Reverse complement sequence

GTGCCACAGTTTAACCTCAAGTACTACTTATCAGGCTATTTACAATGTAAGCTATAGGGCCCGTACCTCAGCCTCAAAACTTGATAAAAACACTTATCTC[G/A]
CAGTGCAAGCACCTATAGTTAGGATACTAAGCCCACAGCCGGTGGACCCCCACGAAAAGGCATTGAGACATCGAGTACTACTCCATTGCCTCCACTTTCC

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 67.80% 31.50% 0.25% 0.36% NA
All Indica  2759 53.90% 45.20% 0.36% 0.62% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 30.50% 69.50% 0.00% 0.00% NA
Indica I  595 55.30% 44.00% 0.00% 0.67% NA
Indica II  465 44.50% 54.40% 0.43% 0.65% NA
Indica III  913 55.30% 44.20% 0.11% 0.33% NA
Indica Intermediate  786 56.60% 41.60% 0.89% 0.89% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 0.00% NA
Intermediate  90 78.90% 20.00% 1.11% 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
vg0502657346 C -> T LOC_Os05g05370.1 upstream_gene_variant ; 789.0bp to feature; MODIFIER silent_mutation Average:87.579; most accessible tissue: Callus, score: 98.453 N N N N
vg0502657346 C -> T LOC_Os05g05370-LOC_Os05g05380 intergenic_region ; MODIFIER silent_mutation Average:87.579; most accessible tissue: Callus, score: 98.453 N N N N
vg0502657346 C -> DEL N N silent_mutation Average:87.579; most accessible tissue: Callus, score: 98.453 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)
vg0502657346 C T 0.07 0.08 0.05 0.05 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502657346 NA 3.24E-07 mr1925_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
vg0502657346 3.11E-06 NA mr1944_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
vg0502657346 5.55E-06 8.73E-06 mr1944_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
vg0502657346 NA 9.91E-06 mr1954_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