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Detailed information for vg0429625218:

Variant ID: vg0429625218 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 29625218
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGAAGTGAGGAGGTAACCGTGAAGGGGACAGGGGCGGGGTATATAACCATGCGGGGGAGAGGTAGGCGACAAAGCAGCGGCGGGGGTGACGTGGTGCGG[A/G]
GGCGGAAAGTGGAGGAGAGTGGGGGAAGGGGGGGAAACCGTGGGTGGTTCTGGAAAACCGGTACGCGAGACGGCCCACCGGCTGGGGAATACCAGAGTCC

Reverse complement sequence

GGACTCTGGTATTCCCCAGCCGGTGGGCCGTCTCGCGTACCGGTTTTCCAGAACCACCCACGGTTTCCCCCCCTTCCCCCACTCTCCTCCACTTTCCGCC[T/C]
CCGCACCACGTCACCCCCGCCGCTGCTTTGTCGCCTACCTCTCCCCCGCATGGTTATATACCCCGCCCCTGTCCCCTTCACGGTTACCTCCTCACTTCAC

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.70% 7.30% 0.00% 0.00% NA
All Indica  2759 88.10% 11.90% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 75.50% 24.50% 0.00% 0.00% NA
Indica Intermediate  786 88.00% 12.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 0.00% 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
vg0429625218 A -> G LOC_Os04g49670.1 upstream_gene_variant ; 3718.0bp to feature; MODIFIER silent_mutation Average:99.902; most accessible tissue: Zhenshan97 flower, score: 99.961 N N N N
vg0429625218 A -> G LOC_Os04g49680.1 upstream_gene_variant ; 86.0bp to feature; MODIFIER silent_mutation Average:99.902; most accessible tissue: Zhenshan97 flower, score: 99.961 N N N N
vg0429625218 A -> G LOC_Os04g49685.1 upstream_gene_variant ; 3170.0bp to feature; MODIFIER silent_mutation Average:99.902; most accessible tissue: Zhenshan97 flower, score: 99.961 N N N N
vg0429625218 A -> G LOC_Os04g49680-LOC_Os04g49685 intergenic_region ; MODIFIER silent_mutation Average:99.902; most accessible tissue: Zhenshan97 flower, score: 99.961 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)
vg0429625218 A G 0.0 0.0 -0.01 0.0 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0429625218 1.90E-08 5.06E-11 Awn_length Ind_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
vg0429625218 7.72E-06 9.98E-06 mr1438 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