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Detailed information for vg0432283565:

Variant ID: vg0432283565 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 32283565
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.63, G: 0.36, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


AAATCCAGGAGAGAAAAAAATAAAGATCTAGACATCGGACGGCACTATCCAAGTTTACCACATCCTGCGGGCAGAGCTCGCGTCACTGCCGTCACACCGT[A/G]
GGGAGTTTAACGCGCCTAAGCATCCACACCCCTCGCCGGGCGTCCGCATCAACGCTGCTGCTCCCGTCGCCGTGCCACCCACTCCACCATCAGTCCATCA

Reverse complement sequence

TGATGGACTGATGGTGGAGTGGGTGGCACGGCGACGGGAGCAGCAGCGTTGATGCGGACGCCCGGCGAGGGGTGTGGATGCTTAGGCGCGTTAAACTCCC[T/C]
ACGGTGTGACGGCAGTGACGCGAGCTCTGCCCGCAGGATGTGGTAAACTTGGATAGTGCCGTCCGATGTCTAGATCTTTATTTTTTTCTCTCCTGGATTT

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 58.40% 40.40% 0.55% 0.70% NA
All Indica  2759 90.00% 7.90% 0.87% 1.16% NA
All Japonica  1512 7.30% 92.70% 0.00% 0.00% NA
Aus  269 19.70% 79.90% 0.00% 0.37% NA
Indica I  595 88.20% 10.90% 0.50% 0.34% NA
Indica II  465 90.30% 8.40% 0.65% 0.65% NA
Indica III  913 92.00% 4.10% 1.42% 2.52% NA
Indica Intermediate  786 88.90% 9.90% 0.64% 0.51% NA
Temperate Japonica  767 1.20% 98.80% 0.00% 0.00% NA
Tropical Japonica  504 17.70% 82.30% 0.00% 0.00% NA
Japonica Intermediate  241 5.40% 94.60% 0.00% 0.00% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 47.80% 50.00% 2.22% 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
vg0432283565 A -> DEL N N silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54190.1 upstream_gene_variant ; 3028.0bp to feature; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54200.1 upstream_gene_variant ; 3096.0bp to feature; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54190.3 upstream_gene_variant ; 2157.0bp to feature; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54190.2 upstream_gene_variant ; 2118.0bp to feature; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54200.2 upstream_gene_variant ; 3096.0bp to feature; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 N N N N
vg0432283565 A -> G LOC_Os04g54190-LOC_Os04g54200 intergenic_region ; MODIFIER silent_mutation Average:99.183; most accessible tissue: Zhenshan97 flag leaf, score: 99.825 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)
vg0432283565 A G 0.04 0.04 0.04 -0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0432283565 NA 2.54E-08 mr1666 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
vg0432283565 NA 1.50E-06 mr1761 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
vg0432283565 NA 4.26E-10 mr1790 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
vg0432283565 8.44E-06 1.25E-06 mr1790 Ind_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
vg0432283565 NA 7.40E-08 mr1084_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
vg0432283565 NA 9.10E-16 mr1133_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
vg0432283565 NA 3.53E-12 mr1151_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
vg0432283565 NA 3.13E-07 mr1302_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
vg0432283565 NA 1.59E-07 mr1399_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
vg0432283565 NA 6.81E-07 mr1418_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
vg0432283565 NA 1.47E-06 mr1488_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
vg0432283565 NA 2.54E-10 mr1506_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
vg0432283565 NA 1.37E-12 mr1521_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
vg0432283565 NA 2.81E-57 mr1558_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
vg0432283565 NA 7.12E-08 mr1604_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
vg0432283565 NA 8.06E-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
vg0432283565 NA 5.36E-12 mr1667_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
vg0432283565 NA 6.15E-06 mr1677_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
vg0432283565 NA 2.00E-19 mr1731_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
vg0432283565 NA 3.90E-07 mr1824_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
vg0432283565 NA 1.02E-07 mr1885_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
vg0432283565 NA 2.39E-19 mr1922_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
vg0432283565 NA 1.23E-22 mr1924_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
vg0432283565 NA 1.32E-09 mr1940_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