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Detailed information for vg0124911355:

Variant ID: vg0124911355 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24911355
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.12, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:


AATGGTTTGTTTTAGTAGTTTAGTAGTAGTACTCGTACTGCTTTGGATCATAGCAACACACATCTTTCCCATGAAAAAACTATGAGTTCTTCAGATTGTG[A/G]
ATATCTAGCTTAATTATGAGACTGCACCACGTTTGCTACCTTTGGATTTGGATGCATGAATCCCGTTTTGCTCGTTCTCGACAGGAGCCGTAAGACACGA

Reverse complement sequence

TCGTGTCTTACGGCTCCTGTCGAGAACGAGCAAAACGGGATTCATGCATCCAAATCCAAAGGTAGCAAACGTGGTGCAGTCTCATAATTAAGCTAGATAT[T/C]
CACAATCTGAAGAACTCATAGTTTTTTCATGGGAAAGATGTGTGTTGCTATGATCCAAAGCAGTACGAGTACTACTACTAAACTACTAAAACAAACCATT

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 73.70% 26.00% 0.19% 0.08% NA
All Indica  2759 99.60% 0.30% 0.07% 0.00% NA
All Japonica  1512 22.00% 77.60% 0.26% 0.13% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.50% 0.25% 0.00% NA
Temperate Japonica  767 1.60% 98.20% 0.26% 0.00% NA
Tropical Japonica  504 56.50% 42.90% 0.40% 0.20% NA
Japonica Intermediate  241 14.50% 85.10% 0.00% 0.41% NA
VI/Aromatic  96 79.20% 20.80% 0.00% 0.00% NA
Intermediate  90 68.90% 25.60% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0124911355 A -> G LOC_Os01g43500.1 downstream_gene_variant ; 3596.0bp to feature; MODIFIER silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0124911355 A -> G LOC_Os01g43510.1 downstream_gene_variant ; 1253.0bp to feature; MODIFIER silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0124911355 A -> G LOC_Os01g43520.1 downstream_gene_variant ; 2125.0bp to feature; MODIFIER silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0124911355 A -> G LOC_Os01g43520.2 downstream_gene_variant ; 2125.0bp to feature; MODIFIER silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0124911355 A -> G LOC_Os01g43510-LOC_Os01g43520 intergenic_region ; MODIFIER silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 N N N N
vg0124911355 A -> DEL N N silent_mutation Average:65.85; most accessible tissue: Zhenshan97 panicle, score: 90.268 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)
vg0124911355 A G 0.04 0.02 0.01 0.0 0.04 0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124911355 NA 9.03E-66 Grain_width All YES Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0124911355 NA 8.61E-85 mr1334 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
vg0124911355 NA 6.06E-32 mr1448 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
vg0124911355 NA 1.00E-06 mr1622 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
vg0124911355 NA 1.26E-73 mr1019_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
vg0124911355 NA 1.12E-94 mr1334_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
vg0124911355 NA 1.48E-42 mr1784_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
vg0124911355 NA 1.00E-50 mr1991_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