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Detailed information for vg0208731146:

Variant ID: vg0208731146 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8731146
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.86, A: 0.13, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTTATATGAATGGCTTTGGTTGCACCGTTTTGTCAAATCTTGTATTGCAAATTACACGAGATCGAGTTAACTTGTATTGACTGCACGTACCTTAAAAT[G/A]
AAACGGCATTTCTTTTTATCTTTCTATTGGAGAGATATGTTCCAAGATTTGCTTTTTTATTGGAGTACGACGAAAGGTATAAGTCAAGAAATTGCAAAAG

Reverse complement sequence

CTTTTGCAATTTCTTGACTTATACCTTTCGTCGTACTCCAATAAAAAAGCAAATCTTGGAACATATCTCTCCAATAGAAAGATAAAAAGAAATGCCGTTT[C/T]
ATTTTAAGGTACGTGCAGTCAATACAAGTTAACTCGATCTCGTGTAATTTGCAATACAAGATTTGACAAAACGGTGCAACCAAAGCCATTCATATAAAAA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 82.50% 17.30% 0.23% 0.00% NA
All Indica  2759 77.50% 22.20% 0.25% 0.00% NA
All Japonica  1512 89.00% 10.80% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 93.80% 6.20% 0.00% 0.00% NA
Indica III  913 51.90% 47.60% 0.44% 0.00% NA
Indica Intermediate  786 81.60% 18.10% 0.38% 0.00% NA
Temperate Japonica  767 89.40% 10.30% 0.26% 0.00% NA
Tropical Japonica  504 87.90% 11.90% 0.20% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 0.00% NA
VI/Aromatic  96 67.70% 32.30% 0.00% 0.00% NA
Intermediate  90 87.80% 11.10% 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
vg0208731146 G -> A LOC_Os02g15550.2 upstream_gene_variant ; 485.0bp to feature; MODIFIER silent_mutation Average:76.357; most accessible tissue: Minghui63 root, score: 86.346 N N N N
vg0208731146 G -> A LOC_Os02g15550.1 upstream_gene_variant ; 485.0bp to feature; MODIFIER silent_mutation Average:76.357; most accessible tissue: Minghui63 root, score: 86.346 N N N N
vg0208731146 G -> A LOC_Os02g15550.3 upstream_gene_variant ; 485.0bp to feature; MODIFIER silent_mutation Average:76.357; most accessible tissue: Minghui63 root, score: 86.346 N N N N
vg0208731146 G -> A LOC_Os02g15560.1 downstream_gene_variant ; 1127.0bp to feature; MODIFIER silent_mutation Average:76.357; most accessible tissue: Minghui63 root, score: 86.346 N N N N
vg0208731146 G -> A LOC_Os02g15550-LOC_Os02g15560 intergenic_region ; MODIFIER silent_mutation Average:76.357; most accessible tissue: Minghui63 root, score: 86.346 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)
vg0208731146 G A 0.03 0.02 0.02 0.01 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208731146 3.33E-07 NA mr1078 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
vg0208731146 NA 6.43E-06 mr1359 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
vg0208731146 6.52E-08 5.54E-08 mr1378 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
vg0208731146 3.98E-06 NA mr1546 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