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Detailed information for vg0502157240:

Variant ID: vg0502157240 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2157240
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.95, T: 0.05, others allele: 0.00, population size: 109. )

Flanking Sequence (100 bp) in Reference Genome:


GTGTTGAGTTGGGGGCTGGACAAGCCAGAGGTCCTCAAGCGATGGTAGTAGCCTTGAGATGCTCACGCTCTGCGCTATGTTTAGATCCAAAGTTTTTCTT[T/C]
AAACTTTCAACTTTTTCATCACATCAAAACTTTCCTATACACACAAACTTCCAACTTTTACATCATAAATTTCAACCAAACACTTCTAATTTTGGTGTGA

Reverse complement sequence

TCACACCAAAATTAGAAGTGTTTGGTTGAAATTTATGATGTAAAAGTTGGAAGTTTGTGTGTATAGGAAAGTTTTGATGTGATGAAAAAGTTGAAAGTTT[A/G]
AAGAAAAACTTTGGATCTAAACATAGCGCAGAGCGTGAGCATCTCAAGGCTACTACCATCGCTTGAGGACCTCTGGCTTGTCCAGCCCCCAACTCAACAC

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 59.30% 40.60% 0.04% 0.00% NA
All Indica  2759 78.50% 21.50% 0.04% 0.00% NA
All Japonica  1512 15.70% 84.30% 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 83.70% 16.30% 0.00% 0.00% NA
Indica III  913 57.80% 42.10% 0.11% 0.00% NA
Indica Intermediate  786 83.60% 16.40% 0.00% 0.00% NA
Temperate Japonica  767 5.10% 94.80% 0.13% 0.00% NA
Tropical Japonica  504 28.20% 71.80% 0.00% 0.00% NA
Japonica Intermediate  241 23.20% 76.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 41.10% 58.90% 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
vg0502157240 T -> C LOC_Os05g04584-LOC_Os05g04600 intergenic_region ; MODIFIER silent_mutation Average:63.254; most accessible tissue: Callus, score: 88.322 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)
vg0502157240 T C -0.02 -0.02 -0.02 -0.02 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502157240 1.22E-06 1.20E-10 mr1794 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
vg0502157240 NA 5.23E-10 mr1030_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
vg0502157240 5.38E-06 1.00E-06 mr1030_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
vg0502157240 NA 9.55E-07 mr1555_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
vg0502157240 NA 9.59E-09 mr1748_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
vg0502157240 NA 8.10E-15 mr1790_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
vg0502157240 NA 2.04E-07 mr1837_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