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Detailed information for vg0232336916:

Variant ID: vg0232336916 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 32336916
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.67, C: 0.32, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


AAATATAAAGGATTTTGGGTGGATGTGACATATACTACTACTACAAATTTGTACATAACTCATGTCTAGATATGTAGTATTAGGATGTGTCATGTCCACC[T/C]
AAAATCACTTATATTTTGTTACGGAGGGAGTATGTGTCATTGCAAATGCACCAATTCAAATAAATGCTATTACAATTCGCCTACTCGTAACCGTGTCAGT

Reverse complement sequence

ACTGACACGGTTACGAGTAGGCGAATTGTAATAGCATTTATTTGAATTGGTGCATTTGCAATGACACATACTCCCTCCGTAACAAAATATAAGTGATTTT[A/G]
GGTGGACATGACACATCCTAATACTACATATCTAGACATGAGTTATGTACAAATTTGTAGTAGTAGTATATGTCACATCCACCCAAAATCCTTTATATTT

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 83.00% 16.90% 0.08% 0.00% NA
All Indica  2759 83.50% 16.50% 0.07% 0.00% NA
All Japonica  1512 99.30% 0.70% 0.00% 0.00% NA
Aus  269 15.60% 84.00% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 65.20% 34.80% 0.00% 0.00% NA
Indica III  913 85.50% 14.50% 0.00% 0.00% NA
Indica Intermediate  786 79.50% 20.20% 0.25% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 89.60% 1.04% 0.00% NA
Intermediate  90 73.30% 26.70% 0.00% 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
vg0232336916 T -> C LOC_Os02g52890.1 upstream_gene_variant ; 993.0bp to feature; MODIFIER silent_mutation Average:75.926; most accessible tissue: Minghui63 root, score: 91.142 N N N N
vg0232336916 T -> C LOC_Os02g52890-LOC_Os02g52900 intergenic_region ; MODIFIER silent_mutation Average:75.926; most accessible tissue: Minghui63 root, score: 91.142 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)
vg0232336916 T C -0.02 -0.01 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0232336916 NA 2.46E-07 mr1415 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
vg0232336916 NA 6.28E-06 mr1445 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
vg0232336916 NA 3.64E-07 mr1453 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
vg0232336916 NA 2.46E-07 mr1567 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
vg0232336916 NA 1.44E-09 mr1593 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
vg0232336916 NA 1.57E-08 mr1829 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
vg0232336916 4.67E-06 NA mr1858 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
vg0232336916 6.75E-06 NA mr1859 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
vg0232336916 NA 6.30E-06 mr1717_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