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Detailed information for vg0519030720:

Variant ID: vg0519030720 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 19030720
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, G: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CGAGTGCGCGCGAGGCTAGGCGGGTGAATGGCGGAGGAGTGGGGGAGGAGGGATTCGAGCAATCGAGCTAGTAGTAGTAATGGCTCGTCACGATCAGAGG[T/G]
GCAGGAGAAGGGGGAGAGTTGAGGAGGGGAGGTGGGAAGAAGAAGAAGAGGAAAATGAATGAGGAGGAGAAGGGACAAGGCCGGGCTCGGTCGGGAGGAA

Reverse complement sequence

TTCCTCCCGACCGAGCCCGGCCTTGTCCCTTCTCCTCCTCATTCATTTTCCTCTTCTTCTTCTTCCCACCTCCCCTCCTCAACTCTCCCCCTTCTCCTGC[A/C]
CCTCTGATCGTGACGAGCCATTACTACTACTAGCTCGATTGCTCGAATCCCTCCTCCCCCACTCCTCCGCCATTCACCCGCCTAGCCTCGCGCGCACTCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.00% 37.40% 0.53% 0.00% NA
All Indica  2759 39.30% 59.90% 0.83% 0.00% NA
All Japonica  1512 96.80% 3.20% 0.00% 0.00% NA
Aus  269 86.20% 13.40% 0.37% 0.00% NA
Indica I  595 53.60% 44.70% 1.68% 0.00% NA
Indica II  465 37.40% 62.20% 0.43% 0.00% NA
Indica III  913 43.80% 55.60% 0.55% 0.00% NA
Indica Intermediate  786 24.20% 75.10% 0.76% 0.00% NA
Temperate Japonica  767 96.30% 3.70% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.80% 1.20% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 63.30% 35.60% 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
vg0519030720 T -> G LOC_Os05g32544.1 5_prime_UTR_variant ; 210.0bp to feature; MODIFIER silent_mutation Average:97.878; most accessible tissue: Callus, score: 98.822 N N N N
vg0519030720 T -> G LOC_Os05g32544.2 5_prime_UTR_variant ; 210.0bp to feature; MODIFIER silent_mutation Average:97.878; most accessible tissue: Callus, score: 98.822 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)
vg0519030720 T G 0.03 0.04 0.03 -0.01 0.02 0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0519030720 NA 3.22E-06 mr1066 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
vg0519030720 1.69E-06 NA mr1711 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
vg0519030720 NA 6.39E-07 mr1830 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
vg0519030720 NA 5.40E-07 mr1846 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
vg0519030720 NA 1.67E-06 mr1199_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
vg0519030720 NA 9.36E-12 mr1830_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
vg0519030720 NA 2.90E-09 mr1846_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
vg0519030720 NA 4.42E-06 mr1869_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
vg0519030720 NA 1.76E-06 mr1951_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