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Detailed information for vg0125383093:

Variant ID: vg0125383093 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25383093
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


TTATATATGCCGCTTGCTTGACTCTGACAAGTGTACGTGTTGTTGTTGTTGTTTTCAGCTAACGTTGGGAAGACGAAGCCGTTGCTGGAGCTGGCGGGGT[A/C]
GAAGGAGAGGCTGACGCTGTGGAAGGCCGACCTGGGCGAGGAAGGCAGCTTCGACGCGGCGATCAGGGGTTGCACGGGCGTGTTCCACGTCGCGACGCCC

Reverse complement sequence

GGGCGTCGCGACGTGGAACACGCCCGTGCAACCCCTGATCGCCGCGTCGAAGCTGCCTTCCTCGCCCAGGTCGGCCTTCCACAGCGTCAGCCTCTCCTTC[T/G]
ACCCCGCCAGCTCCAGCAACGGCTTCGTCTTCCCAACGTTAGCTGAAAACAACAACAACAACACGTACACTTGTCAGAGTCAAGCAAGCGGCATATATAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 85.50% 13.90% 0.53% 0.00% NA
All Indica  2759 99.70% 0.20% 0.07% 0.00% NA
All Japonica  1512 61.20% 37.60% 1.19% 0.00% NA
Aus  269 98.50% 1.10% 0.37% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 99.40% 0.60% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 36.90% 61.80% 1.30% 0.00% NA
Tropical Japonica  504 97.00% 2.00% 0.99% 0.00% NA
Japonica Intermediate  241 63.90% 34.90% 1.24% 0.00% NA
VI/Aromatic  96 31.20% 66.70% 2.08% 0.00% NA
Intermediate  90 77.80% 20.00% 2.22% 0.00% NA

QTN in RiceNavi

Rice quantitative trait nucleotides (QTNs) and inferred QTN effects are from Wei et al., Nature Genetics, 2021.

CategoryVariant IDChromPosGeneMSURAPAlt_Allele_FunctionRef_genoAlt_geno
Seed Morphologyvg0125383093Chr125383093Rd/DFR/OsDfrLOC_Os01g44260Os01g0633500red seed coatAC

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0125383093 A -> C LOC_Os01g44260.1 5_prime_UTR_variant ; 101.0bp to feature; MODIFIER silent_mutation Average:82.7; most accessible tissue: Minghui63 flag leaf, score: 88.574 N N N N
vg0125383093 A -> C LOC_Os01g44270.1 downstream_gene_variant ; 2163.0bp to feature; MODIFIER silent_mutation Average:82.7; most accessible tissue: Minghui63 flag leaf, score: 88.574 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)
vg0125383093 A C 0.03 0.01 0.0 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125383093 3.01E-07 NA mr1219 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
vg0125383093 NA 6.07E-11 mr1712 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
vg0125383093 NA 4.08E-08 mr1946 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
vg0125383093 9.68E-08 NA mr1219_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