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Detailed information for vg0225258286:

Variant ID: vg0225258286 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 25258286
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.90, C: 0.10, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TTCTTCTTTTTAAACACATTACCGCTAACAACACAGCTTACATTCACCATATAAATGCACCCGTACACTAAGGACCATTTAAATCGCAGGATTGCGAAAA[T/C]
GTAGGAATAGGAAAAACGTAGGATTTTGATAGAAATATAAGTGTAAAATAGAGGATTGCAAAACGCAATAAAAACTAATGAATAACCATTTGTTTGAACC

Reverse complement sequence

GGTTCAAACAAATGGTTATTCATTAGTTTTTATTGCGTTTTGCAATCCTCTATTTTACACTTATATTTCTATCAAAATCCTACGTTTTTCCTATTCCTAC[A/G]
TTTTCGCAATCCTGCGATTTAAATGGTCCTTAGTGTACGGGTGCATTTATATGGTGAATGTAAGCTGTGTTGTTAGCGGTAATGTGTTTAAAAAGAAGAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.00% 42.30% 0.57% 3.07% NA
All Indica  2759 62.80% 31.20% 0.83% 5.18% NA
All Japonica  1512 38.70% 61.00% 0.26% 0.07% NA
Aus  269 56.50% 43.50% 0.00% 0.00% NA
Indica I  595 75.80% 22.70% 0.84% 0.67% NA
Indica II  465 53.10% 46.70% 0.22% 0.00% NA
Indica III  913 63.20% 21.90% 1.31% 13.58% NA
Indica Intermediate  786 58.30% 39.20% 0.64% 1.91% NA
Temperate Japonica  767 54.80% 44.70% 0.39% 0.13% NA
Tropical Japonica  504 17.10% 82.70% 0.20% 0.00% NA
Japonica Intermediate  241 32.80% 67.20% 0.00% 0.00% NA
VI/Aromatic  96 36.50% 63.50% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0225258286 T -> DEL N N silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 N N N N
vg0225258286 T -> C LOC_Os02g42020.1 upstream_gene_variant ; 1800.0bp to feature; MODIFIER silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 N N N N
vg0225258286 T -> C LOC_Os02g42030.1 upstream_gene_variant ; 3874.0bp to feature; MODIFIER silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 N N N N
vg0225258286 T -> C LOC_Os02g42020.2 upstream_gene_variant ; 2949.0bp to feature; MODIFIER silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 N N N N
vg0225258286 T -> C LOC_Os02g42020.3 upstream_gene_variant ; 1800.0bp to feature; MODIFIER silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 N N N N
vg0225258286 T -> C LOC_Os02g42020-LOC_Os02g42030 intergenic_region ; MODIFIER silent_mutation Average:88.47; most accessible tissue: Callus, score: 99.316 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)
vg0225258286 T C 0.0 0.02 0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0225258286 3.27E-06 3.27E-06 mr1465 Jap_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
vg0225258286 NA 7.71E-06 mr1042_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
vg0225258286 NA 9.80E-06 mr1164_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
vg0225258286 NA 9.48E-10 mr1457_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