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Detailed information for vg1113279889:

Variant ID: vg1113279889 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 13279889
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:


CAGGCGGGCGGTGTGAGGAGAGGGCGGGAGGCAAGATGCGCGCATGCTGCAATTGGTGAAGGCGGGCGGCCCGCGTGAGCCGCGAAGGGAGGCGGGGACG[C/A]
ACGGGGGTGCGTGCGAGCGTGCCGCGCGCACACATTGGCAGCTGGGTGCGGCACTGTGGACATGTACCTGCGGTGGGCTGGTGGCTTGGGCCTTTCGTGC

Reverse complement sequence

GCACGAAAGGCCCAAGCCACCAGCCCACCGCAGGTACATGTCCACAGTGCCGCACCCAGCTGCCAATGTGTGCGCGCGGCACGCTCGCACGCACCCCCGT[G/T]
CGTCCCCGCCTCCCTTCGCGGCTCACGCGGGCCGCCCGCCTTCACCAATTGCAGCATGCGCGCATCTTGCCTCCCGCCCTCTCCTCACACCGCCCGCCTG

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 90.70% 7.00% 2.35% 0.00% NA
All Indica  2759 85.20% 11.20% 3.62% 0.00% NA
All Japonica  1512 99.70% 0.30% 0.07% 0.00% NA
Aus  269 97.40% 0.40% 2.23% 0.00% NA
Indica I  595 98.70% 0.50% 0.84% 0.00% NA
Indica II  465 47.10% 42.60% 10.32% 0.00% NA
Indica III  913 99.00% 0.30% 0.66% 0.00% NA
Indica Intermediate  786 81.40% 13.40% 5.22% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.20% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 78.90% 16.70% 4.44% 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
vg1113279889 C -> A LOC_Os11g23070.1 downstream_gene_variant ; 572.0bp to feature; MODIFIER silent_mutation Average:83.347; most accessible tissue: Callus, score: 96.852 N N N N
vg1113279889 C -> A LOC_Os11g23080.1 downstream_gene_variant ; 247.0bp to feature; MODIFIER silent_mutation Average:83.347; most accessible tissue: Callus, score: 96.852 N N N N
vg1113279889 C -> A LOC_Os11g23080.2 downstream_gene_variant ; 247.0bp to feature; MODIFIER silent_mutation Average:83.347; most accessible tissue: Callus, score: 96.852 N N N N
vg1113279889 C -> A LOC_Os11g23070-LOC_Os11g23080 intergenic_region ; MODIFIER silent_mutation Average:83.347; most accessible tissue: Callus, score: 96.852 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)
vg1113279889 C A -0.01 -0.02 -0.01 -0.04 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1113279889 NA 1.38E-13 Grain_length All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1113279889 NA 1.12E-08 mr1059 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
vg1113279889 NA 3.07E-11 mr1143 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
vg1113279889 NA 5.23E-10 mr1167 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
vg1113279889 NA 3.62E-09 mr1535 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
vg1113279889 NA 3.93E-08 mr1609 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
vg1113279889 NA 9.45E-10 mr1675 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
vg1113279889 NA 2.55E-09 mr1726 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
vg1113279889 NA 6.38E-07 mr1829 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
vg1113279889 NA 1.50E-09 mr1829 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
vg1113279889 NA 8.43E-10 mr1902 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
vg1113279889 NA 3.33E-07 mr1950 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
vg1113279889 NA 1.55E-10 mr1969 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
vg1113279889 NA 3.12E-11 mr1995 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
vg1113279889 NA 4.02E-06 mr1154_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
vg1113279889 NA 3.45E-08 mr1167_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
vg1113279889 NA 4.43E-09 mr1829_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
vg1113279889 NA 1.01E-09 mr1902_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