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Detailed information for vg0401153085:

Variant ID: vg0401153085 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 1153085
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTAATAATTGGCTATAACTCTTTGAGCAAAGGCCGGAATGCTCTATTCCATTATCTAAAAAGAGGATTACGTTTGATTTCATACTTACATAATACTCC[C/A]
TCAAAGCTTGATTCATATTATAACTTTTTATTTGACTCTTTTTTTAAATTAAACTTATTTAACTCTGAACGAGAATGACTCCATAAAAATCGTGATAGAC

Reverse complement sequence

GTCTATCACGATTTTTATGGAGTCATTCTCGTTCAGAGTTAAATAAGTTTAATTTAAAAAAAGAGTCAAATAAAAAGTTATAATATGAATCAAGCTTTGA[G/T]
GGAGTATTATGTAAGTATGAAATCAAACGTAATCCTCTTTTTAGATAATGGAATAGAGCATTCCGGCCTTTGCTCAAAGAGTTATAGCCAATTATTACAA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.20% 15.70% 0.02% 0.00% NA
All Indica  2759 74.90% 25.00% 0.04% 0.00% NA
All Japonica  1512 96.80% 3.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 36.00% 64.00% 0.00% 0.00% NA
Indica II  465 85.40% 14.60% 0.00% 0.00% NA
Indica III  913 87.40% 12.50% 0.11% 0.00% NA
Indica Intermediate  786 83.70% 16.30% 0.00% 0.00% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 98.40% 1.60% 0.00% 0.00% NA
Japonica Intermediate  241 85.50% 14.50% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0401153085 C -> A LOC_Os04g02910.1 upstream_gene_variant ; 866.0bp to feature; MODIFIER silent_mutation Average:78.958; most accessible tissue: Zhenshan97 flag leaf, score: 90.064 N N N N
vg0401153085 C -> A LOC_Os04g02910.3 upstream_gene_variant ; 1658.0bp to feature; MODIFIER silent_mutation Average:78.958; most accessible tissue: Zhenshan97 flag leaf, score: 90.064 N N N N
vg0401153085 C -> A LOC_Os04g02910.4 upstream_gene_variant ; 866.0bp to feature; MODIFIER silent_mutation Average:78.958; most accessible tissue: Zhenshan97 flag leaf, score: 90.064 N N N N
vg0401153085 C -> A LOC_Os04g02910-LOC_Os04g02920 intergenic_region ; MODIFIER silent_mutation Average:78.958; most accessible tissue: Zhenshan97 flag leaf, score: 90.064 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)
vg0401153085 C A -0.01 0.0 0.01 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0401153085 NA 8.16E-06 mr1086 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
vg0401153085 2.45E-07 NA mr1565 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
vg0401153085 6.76E-07 8.43E-14 mr1565 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
vg0401153085 NA 6.30E-06 mr1878 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
vg0401153085 NA 4.20E-06 mr1558_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
vg0401153085 6.62E-08 NA mr1565_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
vg0401153085 3.21E-09 3.66E-17 mr1565_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