Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0113433238:

Variant ID: vg0113433238 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 13433238
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CAATAGTTGCTTACTATACTATTAATATCTGGGTACATGTCATACACACATTACGTATTGGAGTCCGTGTTGCAGCTGGCTATAGATCTGTAGCCCGCTG[T/C]
TTTTCTCTCTTTCTTTATCCCTTTAAAATATGTTTATAGCTGCTATTGTACCTGCTCTAAGAAGCACAGTGTAGTGGTGGAGTTAAGGGTGCACGATTCC

Reverse complement sequence

GGAATCGTGCACCCTTAACTCCACCACTACACTGTGCTTCTTAGAGCAGGTACAATAGCAGCTATAAACATATTTTAAAGGGATAAAGAAAGAGAGAAAA[A/G]
CAGCGGGCTACAGATCTATAGCCAGCTGCAACACGGACTCCAATACGTAATGTGTGTATGACATGTACCCAGATATTAATAGTATAGTAAGCAACTATTG

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 54.20% 7.90% 3.11% 34.85% NA
All Indica  2759 51.90% 0.40% 1.30% 46.36% NA
All Japonica  1512 67.10% 23.00% 6.68% 3.24% NA
Aus  269 2.20% 0.70% 0.37% 96.65% NA
Indica I  595 34.60% 0.30% 2.52% 62.52% NA
Indica II  465 85.60% 1.10% 1.08% 12.26% NA
Indica III  913 51.60% 0.00% 0.66% 47.75% NA
Indica Intermediate  786 45.50% 0.50% 1.27% 52.67% NA
Temperate Japonica  767 46.90% 42.00% 9.52% 1.56% NA
Tropical Japonica  504 90.50% 1.40% 1.59% 6.55% NA
Japonica Intermediate  241 82.20% 7.90% 8.30% 1.66% NA
VI/Aromatic  96 53.10% 0.00% 2.08% 44.79% NA
Intermediate  90 62.20% 12.20% 7.78% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0113433238 T -> DEL N N silent_mutation Average:51.249; most accessible tissue: Callus, score: 93.333 N N N N
vg0113433238 T -> C LOC_Os01g23870.1 downstream_gene_variant ; 3653.0bp to feature; MODIFIER silent_mutation Average:51.249; most accessible tissue: Callus, score: 93.333 N N N N
vg0113433238 T -> C LOC_Os01g23850-LOC_Os01g23870 intergenic_region ; MODIFIER silent_mutation Average:51.249; most accessible tissue: Callus, score: 93.333 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)
vg0113433238 T C -0.01 -0.02 0.0 0.0 -0.03 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0113433238 9.31E-06 2.48E-14 Spikelet_length All Not 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
vg0113433238 NA 2.28E-07 mr1002 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
vg0113433238 NA 6.61E-06 mr1548 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
vg0113433238 3.24E-06 3.70E-13 mr1712 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
vg0113433238 NA 2.13E-06 mr1794 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
vg0113433238 NA 4.65E-06 mr1910 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
vg0113433238 NA 7.45E-09 mr1977 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
vg0113433238 NA 8.66E-06 mr1051_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
vg0113433238 NA 4.92E-06 mr1627_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