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Detailed information for vg0105774438:

Variant ID: vg0105774438 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5774438
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 345. )

Flanking Sequence (100 bp) in Reference Genome:


GAAAGAGCAAACAAAAACAGGGAGCAGCTACACTACTGTAGGGCAATGCTAAGGATCACAAAATGGGAAGAAACCAAAATGAAAGGAGAAAAAAAAAAGA[A/G]
GGAAAGCAGGGTTCCCTAGCTTAACATGTCTCTCAGTCTCCACCAACTACATTTATCCTTAACCTTACCTACTACTCAACCAGCATGCCCCGTCACGTAC

Reverse complement sequence

GTACGTGACGGGGCATGCTGGTTGAGTAGTAGGTAAGGTTAAGGATAAATGTAGTTGGTGGAGACTGAGAGACATGTTAAGCTAGGGAACCCTGCTTTCC[T/C]
TCTTTTTTTTTTCTCCTTTCATTTTGGTTTCTTCCCATTTTGTGATCCTTAGCATTGCCCTACAGTAGTGTAGCTGCTCCCTGTTTTTGTTTGCTCTTTC

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 96.30% 3.70% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 89.00% 11.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 99.40% 0.60% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.30% 0.00% 0.00% NA
Tropical Japonica  504 77.60% 22.40% 0.00% 0.00% NA
Japonica Intermediate  241 82.20% 17.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0105774438 A -> G LOC_Os01g10840.1 3_prime_UTR_variant ; 333.0bp to feature; MODIFIER silent_mutation Average:86.733; most accessible tissue: Zhenshan97 root, score: 94.852 N N N N
vg0105774438 A -> G LOC_Os01g10810.1 downstream_gene_variant ; 4976.0bp to feature; MODIFIER silent_mutation Average:86.733; most accessible tissue: Zhenshan97 root, score: 94.852 N N N N
vg0105774438 A -> G LOC_Os01g10820.1 downstream_gene_variant ; 2404.0bp to feature; MODIFIER silent_mutation Average:86.733; most accessible tissue: Zhenshan97 root, score: 94.852 N N N N
vg0105774438 A -> G LOC_Os01g10830.1 downstream_gene_variant ; 246.0bp to feature; MODIFIER silent_mutation Average:86.733; most accessible tissue: Zhenshan97 root, score: 94.852 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)
vg0105774438 A G -0.02 -0.01 -0.01 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105774438 5.10E-08 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
vg0105774438 NA 4.72E-07 mr1248_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
vg0105774438 5.67E-06 NA mr1408_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
vg0105774438 NA 7.80E-06 mr1574_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