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Detailed information for vg0105398179:

Variant ID: vg0105398179 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5398179
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


AACGACCTCAACTTGATCTGACGATATCATCCAAAGTTGCAAACTATTTTGTTTATGATAGACCAAATTTTGCAGTGATCGTGTTAGAAAGAGATAAAAA[C/T]
AATTTGAAGGAATTTTGCATTTTTACCTCGAAATATAACCAGGCCTGTGAACGTTGTCTGCTGGAAGCGCGCAATTTGTTTGGAATTCATGGCGAAGGTT

Reverse complement sequence

AACCTTCGCCATGAATTCCAAACAAATTGCGCGCTTCCAGCAGACAACGTTCACAGGCCTGGTTATATTTCGAGGTAAAAATGCAAAATTCCTTCAAATT[G/A]
TTTTTATCTCTTTCTAACACGATCACTGCAAAATTTGGTCTATCATAAACAAAATAGTTTGCAACTTTGGATGATATCGTCAGATCAAGTTGAGGTCGTT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 74.40% 25.50% 0.15% 0.00% NA
All Indica  2759 98.70% 1.20% 0.11% 0.00% NA
All Japonica  1512 28.60% 71.20% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 98.70% 1.20% 0.11% 0.00% NA
Indica Intermediate  786 96.90% 2.80% 0.25% 0.00% NA
Temperate Japonica  767 47.50% 52.40% 0.13% 0.00% NA
Tropical Japonica  504 4.00% 95.80% 0.20% 0.00% NA
Japonica Intermediate  241 19.90% 79.70% 0.41% 0.00% NA
VI/Aromatic  96 30.20% 69.80% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0105398179 C -> T LOC_Os01g10250.1 upstream_gene_variant ; 3765.0bp to feature; MODIFIER silent_mutation Average:81.081; most accessible tissue: Minghui63 flag leaf, score: 97.949 N N N N
vg0105398179 C -> T LOC_Os01g10250.2 upstream_gene_variant ; 4311.0bp to feature; MODIFIER silent_mutation Average:81.081; most accessible tissue: Minghui63 flag leaf, score: 97.949 N N N N
vg0105398179 C -> T LOC_Os01g10250.3 upstream_gene_variant ; 3765.0bp to feature; MODIFIER silent_mutation Average:81.081; most accessible tissue: Minghui63 flag leaf, score: 97.949 N N N N
vg0105398179 C -> T LOC_Os01g10260.1 downstream_gene_variant ; 3222.0bp to feature; MODIFIER silent_mutation Average:81.081; most accessible tissue: Minghui63 flag leaf, score: 97.949 N N N N
vg0105398179 C -> T LOC_Os01g10250-LOC_Os01g10260 intergenic_region ; MODIFIER silent_mutation Average:81.081; most accessible tissue: Minghui63 flag leaf, score: 97.949 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)
vg0105398179 C T 0.01 0.01 0.02 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105398179 NA 2.82E-06 mr1408 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
vg0105398179 NA 1.07E-09 mr1578 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
vg0105398179 2.41E-06 6.96E-39 mr1891 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
vg0105398179 NA 1.16E-10 mr1379_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
vg0105398179 NA 7.27E-17 mr1416_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
vg0105398179 NA 1.86E-20 mr1627_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