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Detailed information for vg0324614045:

Variant ID: vg0324614045 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 24614045
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 119. )

Flanking Sequence (100 bp) in Reference Genome:


GGATGTATCGATGACGCGTCGTTCCTCGGCTTGTCATCACGCACTGATCGACGCACACATGAGAGAGACTGAGAGAGAGAGATCGGGGGGAATGGAATCA[A/G]
TGTCGCCGCGGGCGCCGATCTCCTCCTGGCTTCGCCCACGAACGACTTGTCTCTCCCGCGCCGCACGCCGTTTCGTCCGCCATGTGTCCGTGGCCGCGGG

Reverse complement sequence

CCCGCGGCCACGGACACATGGCGGACGAAACGGCGTGCGGCGCGGGAGAGACAAGTCGTTCGTGGGCGAAGCCAGGAGGAGATCGGCGCCCGCGGCGACA[T/C]
TGATTCCATTCCCCCCGATCTCTCTCTCTCAGTCTCTCTCATGTGTGCGTCGATCAGTGCGTGATGACAAGCCGAGGAACGACGCGTCATCGATACATCC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.60% 15.30% 0.08% 0.00% NA
All Indica  2759 79.60% 20.20% 0.14% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.00% NA
Aus  269 46.10% 53.90% 0.00% 0.00% NA
Indica I  595 89.70% 10.10% 0.17% 0.00% NA
Indica II  465 94.20% 5.40% 0.43% 0.00% NA
Indica III  913 68.70% 31.20% 0.11% 0.00% NA
Indica Intermediate  786 76.10% 23.90% 0.00% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0324614045 A -> G LOC_Os03g43870.1 upstream_gene_variant ; 4075.0bp to feature; MODIFIER silent_mutation Average:92.826; most accessible tissue: Minghui63 panicle, score: 98.973 N N N N
vg0324614045 A -> G LOC_Os03g43880.1 downstream_gene_variant ; 2277.0bp to feature; MODIFIER silent_mutation Average:92.826; most accessible tissue: Minghui63 panicle, score: 98.973 N N N N
vg0324614045 A -> G LOC_Os03g43870-LOC_Os03g43880 intergenic_region ; MODIFIER silent_mutation Average:92.826; most accessible tissue: Minghui63 panicle, score: 98.973 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)
vg0324614045 A G 0.1 0.08 0.08 0.06 0.06 0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0324614045 NA 9.80E-06 mr1542 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
vg0324614045 2.45E-06 NA mr1687 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
vg0324614045 NA 3.31E-10 mr1739 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
vg0324614045 NA 1.20E-13 mr1739 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
vg0324614045 NA 1.78E-06 mr1006_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
vg0324614045 NA 1.47E-06 mr1257_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
vg0324614045 NA 1.48E-06 mr1542_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
vg0324614045 NA 1.00E-08 mr1739_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