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Detailed information for vg0501153947:

Variant ID: vg0501153947 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1153947
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:


CCGCACGAGAGAAAAAGGTGAGGCATCGTTTACTCCTCTCGTTAGTTACGATTGGCGATTGGCGAGGTCCACAGTGGGAGGCGATTAAAGATTGCGAACC[G/A]
CCGCAACTGTGTGAACCGGCAAAGGCGTAATCGAAGCCAAAACGACAAGAAAAATAACAGATTTTCAGGACTAGTTAGGCTACCAATTTACTTACTGAGT

Reverse complement sequence

ACTCAGTAAGTAAATTGGTAGCCTAACTAGTCCTGAAAATCTGTTATTTTTCTTGTCGTTTTGGCTTCGATTACGCCTTTGCCGGTTCACACAGTTGCGG[C/T]
GGTTCGCAATCTTTAATCGCCTCCCACTGTGGACCTCGCCAATCGCCAATCGTAACTAACGAGAGGAGTAAACGATGCCTCACCTTTTTCTCTCGTGCGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 70.40% 29.60% 0.06% 0.00% NA
All Indica  2759 50.60% 49.30% 0.11% 0.00% NA
All Japonica  1512 99.40% 0.60% 0.00% 0.00% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 27.40% 72.60% 0.00% 0.00% NA
Indica II  465 37.00% 62.80% 0.22% 0.00% NA
Indica III  913 76.10% 23.80% 0.11% 0.00% NA
Indica Intermediate  786 46.70% 53.20% 0.13% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 74.40% 25.60% 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
vg0501153947 G -> A LOC_Os05g03040.1 downstream_gene_variant ; 2021.0bp to feature; MODIFIER silent_mutation Average:74.818; most accessible tissue: Zhenshan97 young leaf, score: 97.615 N N N N
vg0501153947 G -> A LOC_Os05g03040.2 downstream_gene_variant ; 2021.0bp to feature; MODIFIER silent_mutation Average:74.818; most accessible tissue: Zhenshan97 young leaf, score: 97.615 N N N N
vg0501153947 G -> A LOC_Os05g03040.3 downstream_gene_variant ; 2021.0bp to feature; MODIFIER silent_mutation Average:74.818; most accessible tissue: Zhenshan97 young leaf, score: 97.615 N N N N
vg0501153947 G -> A LOC_Os05g03030-LOC_Os05g03040 intergenic_region ; MODIFIER silent_mutation Average:74.818; most accessible tissue: Zhenshan97 young leaf, score: 97.615 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)
vg0501153947 G A -0.03 0.03 0.02 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501153947 NA 2.91E-06 mr1136 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
vg0501153947 NA 6.59E-06 mr1280 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
vg0501153947 NA 3.78E-07 mr1318 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
vg0501153947 NA 9.78E-06 mr1434 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
vg0501153947 NA 1.06E-08 mr1510 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
vg0501153947 NA 9.43E-06 mr1534 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
vg0501153947 3.59E-06 7.67E-08 mr1630 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
vg0501153947 NA 1.90E-06 mr1691 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
vg0501153947 NA 6.90E-06 mr1693 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
vg0501153947 NA 3.17E-07 mr1728 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
vg0501153947 NA 2.34E-06 mr1729 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
vg0501153947 NA 5.54E-11 mr1751 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
vg0501153947 NA 1.56E-06 mr1751 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
vg0501153947 4.55E-06 4.55E-06 mr1779 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
vg0501153947 NA 8.84E-06 mr1782 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
vg0501153947 NA 4.11E-18 mr1807 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
vg0501153947 NA 1.60E-07 mr1807 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