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Detailed information for vg1122897896:

Variant ID: vg1122897896 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 22897896
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: 130. )

Flanking Sequence (100 bp) in Reference Genome:


AACACATCTATACCTAATTAAAAAATAAGTAAGGCTTCCGGTTGATTTTTTTCGTCCGTCATTAAAGGGTGGGCCCACGTGATTATTTCGCCGCTAATCC[G/A]
TGAATCCGGATGCATTACGGCGATCGATCTCTGACGCTCCGCAAACAAAAGAGAAACGAAAAAAAGAAAAACCAAGCGAGCAGCCCAGCCAAGACGGCAG

Reverse complement sequence

CTGCCGTCTTGGCTGGGCTGCTCGCTTGGTTTTTCTTTTTTTCGTTTCTCTTTTGTTTGCGGAGCGTCAGAGATCGATCGCCGTAATGCATCCGGATTCA[C/T]
GGATTAGCGGCGAAATAATCACGTGGGCCCACCCTTTAATGACGGACGAAAAAAATCAACCGGAAGCCTTACTTATTTTTTAATTAGGTATAGATGTGTT

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 80.70% 5.00% 0.19% 14.07% NA
All Indica  2759 87.80% 8.10% 0.14% 3.95% NA
All Japonica  1512 63.60% 0.10% 0.33% 35.91% NA
Aus  269 96.70% 3.00% 0.00% 0.37% NA
Indica I  595 96.10% 0.30% 0.00% 3.53% NA
Indica II  465 72.00% 27.50% 0.43% 0.00% NA
Indica III  913 92.00% 2.20% 0.00% 5.81% NA
Indica Intermediate  786 86.00% 9.30% 0.25% 4.45% NA
Temperate Japonica  767 57.50% 0.00% 0.00% 42.50% NA
Tropical Japonica  504 62.10% 0.20% 0.99% 36.71% NA
Japonica Intermediate  241 86.30% 0.40% 0.00% 13.28% NA
VI/Aromatic  96 94.80% 0.00% 0.00% 5.21% NA
Intermediate  90 88.90% 3.30% 0.00% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1122897896 G -> A LOC_Os11g38630.1 upstream_gene_variant ; 2788.0bp to feature; MODIFIER silent_mutation Average:69.867; most accessible tissue: Zhenshan97 flower, score: 91.09 N N N N
vg1122897896 G -> A LOC_Os11g38620-LOC_Os11g38630 intergenic_region ; MODIFIER silent_mutation Average:69.867; most accessible tissue: Zhenshan97 flower, score: 91.09 N N N N
vg1122897896 G -> DEL N N silent_mutation Average:69.867; most accessible tissue: Zhenshan97 flower, score: 91.09 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)
vg1122897896 G A 0.01 0.02 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
vg1122897896 NA 7.87E-07 mr1304 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
vg1122897896 5.51E-09 4.59E-12 mr1310 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
vg1122897896 NA 2.00E-07 mr1498 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
vg1122897896 NA 8.88E-06 mr1668 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
vg1122897896 7.01E-07 5.92E-11 mr1889 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
vg1122897896 1.59E-08 1.59E-08 mr1926 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
vg1122897896 NA 1.27E-09 mr1934 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
vg1122897896 NA 2.31E-07 mr1310_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
vg1122897896 NA 2.71E-06 mr1540_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
vg1122897896 NA 4.02E-06 mr1732_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