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Detailed information for vg0228081584:

Variant ID: vg0228081584 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 28081584
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


TTTCCCTTCTTTCCCTCCTCTCGAAAGAAGTCGCCTTTGGAACCCCAAAGGACCAAGAACGCCCAAGAACAAACTTGAACACCCTAAGTGACAAAAAGGA[T/C]
TAGGTTTCTGGAGGACTATCCCAAATTTAATTTCTAGAAATCGAAAAATAGAACGATTTGTAGTTCAATTATACCTGTCGTTGCACTTGCACCTCACCAG

Reverse complement sequence

CTGGTGAGGTGCAAGTGCAACGACAGGTATAATTGAACTACAAATCGTTCTATTTTTCGATTTCTAGAAATTAAATTTGGGATAGTCCTCCAGAAACCTA[A/G]
TCCTTTTTGTCACTTAGGGTGTTCAAGTTTGTTCTTGGGCGTTCTTGGTCCTTTGGGGTTCCAAAGGCGACTTCTTTCGAGAGGAGGGAAAGAAGGGAAA

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 50.40% 49.20% 0.25% 0.08% NA
All Indica  2759 85.20% 14.30% 0.36% 0.14% NA
All Japonica  1512 0.30% 99.70% 0.00% 0.00% NA
Aus  269 1.90% 97.80% 0.37% 0.00% NA
Indica I  595 96.80% 3.20% 0.00% 0.00% NA
Indica II  465 90.30% 9.00% 0.43% 0.22% NA
Indica III  913 77.40% 22.20% 0.22% 0.11% NA
Indica Intermediate  786 82.30% 16.70% 0.76% 0.25% NA
Temperate Japonica  767 0.30% 99.70% 0.00% 0.00% NA
Tropical Japonica  504 0.40% 99.60% 0.00% 0.00% NA
Japonica Intermediate  241 0.00% 100.00% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 25.60% 73.30% 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
vg0228081584 T -> DEL N N silent_mutation Average:93.989; most accessible tissue: Zhenshan97 flower, score: 96.948 N N N N
vg0228081584 T -> C LOC_Os02g46090.1 upstream_gene_variant ; 4797.0bp to feature; MODIFIER silent_mutation Average:93.989; most accessible tissue: Zhenshan97 flower, score: 96.948 N N N N
vg0228081584 T -> C LOC_Os02g46080.1 intron_variant ; MODIFIER silent_mutation Average:93.989; most accessible tissue: Zhenshan97 flower, score: 96.948 N N N N
vg0228081584 T -> C LOC_Os02g46080.2 intron_variant ; MODIFIER silent_mutation Average:93.989; most accessible tissue: Zhenshan97 flower, score: 96.948 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)
vg0228081584 T C -0.01 -0.02 -0.02 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0228081584 NA 8.60E-51 mr1063 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
vg0228081584 NA 1.70E-52 mr1090 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
vg0228081584 NA 2.45E-47 mr1121 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
vg0228081584 NA 2.84E-09 mr1151 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
vg0228081584 NA 5.77E-16 mr1164 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
vg0228081584 NA 1.14E-30 mr1208 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
vg0228081584 NA 1.03E-06 mr1717 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
vg0228081584 NA 1.75E-41 mr1721 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
vg0228081584 NA 3.55E-12 mr1914 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
vg0228081584 NA 3.94E-15 mr1916 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
vg0228081584 NA 9.43E-52 mr1063_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
vg0228081584 NA 6.48E-23 mr1164_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
vg0228081584 NA 2.69E-25 mr1244_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
vg0228081584 NA 3.80E-17 mr1260_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
vg0228081584 NA 3.67E-30 mr1580_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
vg0228081584 NA 4.30E-12 mr1666_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
vg0228081584 NA 9.94E-29 mr1825_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