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Detailed information for vg0428859732:

Variant ID: vg0428859732 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 28859732
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCCTCACATGTGGATACAATGGAGTTCATGTGGATCCCACGCTGACTCAGTTGGATTGACCGTAGTTAACATCAGTCAAAACCAGACACAAAATTATC[C/T]
TAGGACCTCAGGTACCTAGGTATTGTAAGTTGAGGGACACGTTATATCGGATATTGGGGTTGACCGATAAGATTTAAACTCAACGTCAAGATGAAGGATT

Reverse complement sequence

AATCCTTCATCTTGACGTTGAGTTTAAATCTTATCGGTCAACCCCAATATCCGATATAACGTGTCCCTCAACTTACAATACCTAGGTACCTGAGGTCCTA[G/A]
GATAATTTTGTGTCTGGTTTTGACTGATGTTAACTACGGTCAATCCAACTGAGTCAGCGTGGGATCCACATGAACTCCATTGTATCCACATGTGAGGGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.30% 6.30% 3.15% 0.23% NA
All Indica  2759 99.50% 0.30% 0.18% 0.00% NA
All Japonica  1512 72.10% 18.30% 8.86% 0.73% NA
Aus  269 98.10% 0.00% 1.86% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 98.70% 0.90% 0.38% 0.00% NA
Temperate Japonica  767 60.00% 25.20% 13.69% 1.17% NA
Tropical Japonica  504 92.30% 4.60% 2.98% 0.20% NA
Japonica Intermediate  241 68.50% 25.30% 5.81% 0.41% NA
VI/Aromatic  96 89.60% 9.40% 1.04% 0.00% NA
Intermediate  90 93.30% 2.20% 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
vg0428859732 C -> DEL N N silent_mutation Average:95.828; most accessible tissue: Minghui63 flag leaf, score: 97.504 N N N N
vg0428859732 C -> T LOC_Os04g48390.1 upstream_gene_variant ; 2868.0bp to feature; MODIFIER silent_mutation Average:95.828; most accessible tissue: Minghui63 flag leaf, score: 97.504 N N N N
vg0428859732 C -> T LOC_Os04g48380.1 downstream_gene_variant ; 4777.0bp to feature; MODIFIER silent_mutation Average:95.828; most accessible tissue: Minghui63 flag leaf, score: 97.504 N N N N
vg0428859732 C -> T LOC_Os04g48380-LOC_Os04g48390 intergenic_region ; MODIFIER silent_mutation Average:95.828; most accessible tissue: Minghui63 flag leaf, score: 97.504 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)
vg0428859732 C T 0.01 -0.02 -0.01 -0.01 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0428859732 3.27E-09 NA Grain_weight All YES 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
vg0428859732 6.36E-06 NA mr1010_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
vg0428859732 2.21E-06 1.22E-15 mr1842_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