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Detailed information for vg1121374252:

Variant ID: vg1121374252 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21374252
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:


ACGTCATCAAAGGGGCCGGCGCAGACAGGCGGGCCTCACACGTCAGTGGGTCAAGGGGAGCGGTCCACCGTGGACCAGAACCACGAGGTGGTCCACCGCC[G/A]
GTCCACGGGAACCGACGGCCCAAATCGGCCAAAACCGATCGGGCGGCCATAGAGTGGCGCGGCCAGGGCACAGGCGCGGCTCAAAGCTGGCCCGGCTGAG

Reverse complement sequence

CTCAGCCGGGCCAGCTTTGAGCCGCGCCTGTGCCCTGGCCGCGCCACTCTATGGCCGCCCGATCGGTTTTGGCCGATTTGGGCCGTCGGTTCCCGTGGAC[C/T]
GGCGGTGGACCACCTCGTGGTTCTGGTCCACGGTGGACCGCTCCCCTTGACCCACTGACGTGTGAGGCCCGCCTGTCTGCGCCGGCCCCTTTGATGACGT

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 70.40% 27.30% 0.83% 1.48% NA
All Indica  2759 54.80% 43.80% 0.94% 0.47% NA
All Japonica  1512 94.40% 4.50% 0.20% 0.93% NA
Aus  269 81.80% 0.40% 2.23% 15.61% NA
Indica I  595 42.20% 55.60% 2.18% 0.00% NA
Indica II  465 44.10% 52.50% 1.29% 2.15% NA
Indica III  913 65.20% 34.20% 0.55% 0.11% NA
Indica Intermediate  786 58.50% 41.00% 0.25% 0.25% NA
Temperate Japonica  767 93.60% 4.60% 0.13% 1.69% NA
Tropical Japonica  504 95.80% 4.00% 0.00% 0.20% NA
Japonica Intermediate  241 93.80% 5.40% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 81.10% 13.30% 4.44% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121374252 G -> A LOC_Os11g36300.1 upstream_gene_variant ; 622.0bp to feature; MODIFIER silent_mutation Average:64.407; most accessible tissue: Zhenshan97 young leaf, score: 84.035 N N N N
vg1121374252 G -> A LOC_Os11g36290.1 downstream_gene_variant ; 1801.0bp to feature; MODIFIER silent_mutation Average:64.407; most accessible tissue: Zhenshan97 young leaf, score: 84.035 N N N N
vg1121374252 G -> A LOC_Os11g36290-LOC_Os11g36300 intergenic_region ; MODIFIER silent_mutation Average:64.407; most accessible tissue: Zhenshan97 young leaf, score: 84.035 N N N N
vg1121374252 G -> DEL N N silent_mutation Average:64.407; most accessible tissue: Zhenshan97 young leaf, score: 84.035 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)
vg1121374252 G A -0.01 -0.01 -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
vg1121374252 NA 2.44E-06 mr1698 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
vg1121374252 4.54E-06 8.64E-09 mr1517_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
vg1121374252 NA 5.64E-06 mr1577_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
vg1121374252 3.25E-06 2.60E-08 mr1698_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
vg1121374252 2.05E-06 2.05E-06 mr1908_2 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
vg1121374252 2.75E-06 2.61E-06 mr1994_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