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Detailed information for vg0528518287:

Variant ID: vg0528518287 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 28518287
Reference Allele: AAlternative Allele: T
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.69, A: 0.31, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:


TGACGAAGACTTGACGTAAGCACACGTAATCCCCTCAAAAAAAAAGAAAAAGAAGAAGAAGAAGAAAAGAAAACTAAAATAACTGCCTAGTGCAATACAA[A/T]
TGGCTCGGGCGGGCATAGGCCCGGTGACCACGCGCGGGCGACTCAGGAGAAACCTAGCGCCACCGCCGGAGCGCGTCACCGGAGCACCGTGCGGCCATCC

Reverse complement sequence

GGATGGCCGCACGGTGCTCCGGTGACGCGCTCCGGCGGTGGCGCTAGGTTTCTCCTGAGTCGCCCGCGCGTGGTCACCGGGCCTATGCCCGCCCGAGCCA[T/A]
TTGTATTGCACTAGGCAGTTATTTTAGTTTTCTTTTCTTCTTCTTCTTCTTTTTCTTTTTTTTTGAGGGGATTACGTGTGCTTACGTCAAGTCTTCGTCA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 71.00% 28.90% 0.13% 0.00% NA
All Indica  2759 98.60% 1.20% 0.14% 0.00% NA
All Japonica  1512 17.50% 82.40% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.10% 0.22% 0.00% NA
Indica Intermediate  786 97.80% 1.90% 0.25% 0.00% NA
Temperate Japonica  767 1.80% 98.00% 0.13% 0.00% NA
Tropical Japonica  504 36.70% 63.30% 0.00% 0.00% NA
Japonica Intermediate  241 27.40% 72.60% 0.00% 0.00% NA
VI/Aromatic  96 42.70% 57.30% 0.00% 0.00% NA
Intermediate  90 64.40% 34.40% 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
vg0528518287 A -> T LOC_Os05g49720-LOC_Os05g49730 intergenic_region ; MODIFIER silent_mutation Average:93.16; most accessible tissue: Zhenshan97 flag leaf, score: 96.46 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)
vg0528518287 A T 0.02 0.05 0.04 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528518287 NA 1.95E-17 mr1133 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
vg0528518287 NA 1.03E-07 mr1227 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
vg0528518287 NA 6.07E-18 mr1304 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
vg0528518287 8.97E-07 NA mr1696 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
vg0528518287 NA 1.18E-06 mr1696 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
vg0528518287 NA 3.31E-10 mr1714 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