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Detailed information for vg0226516840:

Variant ID: vg0226516840 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 26516840
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.09, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGCCCTTTCACGGTACAGCTAGACAGCGACACAAGCAGGCATCAATGCATCGTGTATTCGTGTATCGTCGTCTCTTCTGGTACAGAGGACTTACTATA[G/A]
CCTGTATGACAAATAGGAGCTCGTCTTCTCGTATGGAGGAGTACTACGTGTGTGGCTGCCTTGGCTAGCTGGTGTATGATGTTGTACCTTGCACTCAACA

Reverse complement sequence

TGTTGAGTGCAAGGTACAACATCATACACCAGCTAGCCAAGGCAGCCACACACGTAGTACTCCTCCATACGAGAAGACGAGCTCCTATTTGTCATACAGG[C/T]
TATAGTAAGTCCTCTGTACCAGAAGAGACGACGATACACGAATACACGATGCATTGATGCCTGCTTGTGTCGCTGTCTAGCTGTACCGTGAAAGGGCTTT

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 56.10% 43.60% 0.11% 0.21% NA
All Indica  2759 85.20% 14.50% 0.11% 0.25% NA
All Japonica  1512 0.60% 99.20% 0.00% 0.20% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 93.60% 5.90% 0.50% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 72.10% 27.60% 0.00% 0.33% NA
Indica Intermediate  786 86.50% 13.00% 0.00% 0.51% NA
Temperate Japonica  767 0.40% 99.60% 0.00% 0.00% NA
Tropical Japonica  504 1.20% 98.60% 0.00% 0.20% NA
Japonica Intermediate  241 0.00% 99.20% 0.00% 0.83% NA
VI/Aromatic  96 4.20% 94.80% 1.04% 0.00% NA
Intermediate  90 35.60% 63.30% 1.11% 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
vg0226516840 G -> A LOC_Os02g43930.1 upstream_gene_variant ; 2486.0bp to feature; MODIFIER silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 N N N N
vg0226516840 G -> A LOC_Os02g43930.2 upstream_gene_variant ; 2486.0bp to feature; MODIFIER silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 N N N N
vg0226516840 G -> A LOC_Os02g43930.3 upstream_gene_variant ; 2486.0bp to feature; MODIFIER silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 N N N N
vg0226516840 G -> A LOC_Os02g43920.1 downstream_gene_variant ; 995.0bp to feature; MODIFIER silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 N N N N
vg0226516840 G -> A LOC_Os02g43920-LOC_Os02g43930 intergenic_region ; MODIFIER silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 N N N N
vg0226516840 G -> DEL N N silent_mutation Average:79.328; most accessible tissue: Zhenshan97 root, score: 91.881 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)
vg0226516840 G A 0.0 -0.01 0.0 -0.06 -0.06 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0226516840 1.02E-10 1.84E-14 Awn_length Ind_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
vg0226516840 NA 6.31E-18 mr1336_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
vg0226516840 NA 1.80E-16 mr1342_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