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Detailed information for vg0430452456:

Variant ID: vg0430452456 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 30452456
Reference Allele: GAlternative Allele: C
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, G: 0.02, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AGGTGGAATTATTGTGAGCTGTGATGACCATTCAAATTTGCAGGGGAGCTCTTGTGAAATTCTATTTGGAGCGCAAGAAAATCACATGAGATATTCAGTT[G/C]
ACATTCATTGCAAAAATTACAATGACGAATTACCATCTCATCAGGAGGTTCAGAACATGTGAGCACAACACACGTCTCATCAGACCCCGCTTCTTTCTCG

Reverse complement sequence

CGAGAAAGAAGCGGGGTCTGATGAGACGTGTGTTGTGCTCACATGTTCTGAACCTCCTGATGAGATGGTAATTCGTCATTGTAATTTTTGCAATGAATGT[C/G]
AACTGAATATCTCATGTGATTTTCTTGCGCTCCAAATAGAATTTCACAAGAGCTCCCCTGCAAATTTGAATGGTCATCACAGCTCACAATAATTCCACCT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.10% 47.90% 0.04% 0.00% NA
All Indica  2759 63.70% 36.20% 0.04% 0.00% NA
All Japonica  1512 27.90% 72.10% 0.00% 0.00% NA
Aus  269 89.20% 10.80% 0.00% 0.00% NA
Indica I  595 49.40% 50.40% 0.17% 0.00% NA
Indica II  465 75.70% 24.30% 0.00% 0.00% NA
Indica III  913 62.50% 37.50% 0.00% 0.00% NA
Indica Intermediate  786 68.80% 31.20% 0.00% 0.00% NA
Temperate Japonica  767 6.00% 94.00% 0.00% 0.00% NA
Tropical Japonica  504 50.80% 49.20% 0.00% 0.00% NA
Japonica Intermediate  241 49.80% 50.20% 0.00% 0.00% NA
VI/Aromatic  96 2.10% 96.90% 1.04% 0.00% NA
Intermediate  90 43.30% 56.70% 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
vg0430452456 G -> C LOC_Os04g51410.1 upstream_gene_variant ; 1067.0bp to feature; MODIFIER silent_mutation Average:92.853; most accessible tissue: Callus, score: 98.335 N N N N
vg0430452456 G -> C LOC_Os04g51420.1 downstream_gene_variant ; 2011.0bp to feature; MODIFIER silent_mutation Average:92.853; most accessible tissue: Callus, score: 98.335 N N N N
vg0430452456 G -> C LOC_Os04g51410-LOC_Os04g51420 intergenic_region ; MODIFIER silent_mutation Average:92.853; most accessible tissue: Callus, score: 98.335 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)
vg0430452456 G C 0.0 0.05 0.03 0.01 0.06 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0430452456 NA 4.11E-09 mr1174 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
vg0430452456 NA 2.51E-09 mr1174 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
vg0430452456 1.94E-06 8.36E-09 mr1347 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
vg0430452456 NA 2.22E-09 mr1347 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
vg0430452456 5.74E-08 NA mr1745 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
vg0430452456 NA 3.18E-06 mr1745 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
vg0430452456 NA 1.06E-06 mr1064_2 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
vg0430452456 NA 1.62E-07 mr1174_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
vg0430452456 6.50E-10 NA mr1745_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
vg0430452456 3.29E-07 4.82E-11 mr1745_2 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