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Detailed information for vg0405362835:

Variant ID: vg0405362835 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 5362835
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, A: 0.07, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


AAATGATAATTACATAATTTCTTTTTAATAAAATGAATGATAAAACGTTGTTAAAAAATATGGAGGAAGTAGTATATTCCAGCTGAAACTAGCTAGGACA[C/A]
GTTCTTCTGCCTTGTTTACGTAGTGATGTCGTCCATGGCATAGGTGGGGGCTCGTGGACAGGTCTATCTGTAGCATTTTAAAAAGCTATCGTGATTCTCT

Reverse complement sequence

AGAGAATCACGATAGCTTTTTAAAATGCTACAGATAGACCTGTCCACGAGCCCCCACCTATGCCATGGACGACATCACTACGTAAACAAGGCAGAAGAAC[G/T]
TGTCCTAGCTAGTTTCAGCTGGAATATACTACTTCCTCCATATTTTTTAACAACGTTTTATCATTCATTTTATTAAAAAGAAATTATGTAATTATCATTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 59.00% 37.20% 2.84% 0.97% NA
All Indica  2759 84.40% 9.40% 4.57% 1.59% NA
All Japonica  1512 4.20% 95.70% 0.07% 0.07% NA
Aus  269 98.10% 0.70% 1.12% 0.00% NA
Indica I  595 85.20% 5.20% 7.90% 1.68% NA
Indica II  465 78.50% 15.90% 4.52% 1.08% NA
Indica III  913 89.60% 6.10% 2.19% 2.08% NA
Indica Intermediate  786 81.30% 12.60% 4.83% 1.27% NA
Temperate Japonica  767 0.50% 99.50% 0.00% 0.00% NA
Tropical Japonica  504 9.30% 90.50% 0.20% 0.00% NA
Japonica Intermediate  241 5.00% 94.60% 0.00% 0.41% NA
VI/Aromatic  96 85.40% 11.50% 2.08% 1.04% NA
Intermediate  90 54.40% 43.30% 2.22% 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
vg0405362835 C -> DEL N N silent_mutation Average:67.026; most accessible tissue: Callus, score: 93.852 N N N N
vg0405362835 C -> A LOC_Os04g09980.1 upstream_gene_variant ; 3981.0bp to feature; MODIFIER silent_mutation Average:67.026; most accessible tissue: Callus, score: 93.852 N N N N
vg0405362835 C -> A LOC_Os04g09960.1 downstream_gene_variant ; 3096.0bp to feature; MODIFIER silent_mutation Average:67.026; most accessible tissue: Callus, score: 93.852 N N N N
vg0405362835 C -> A LOC_Os04g09960-LOC_Os04g09980 intergenic_region ; MODIFIER silent_mutation Average:67.026; most accessible tissue: Callus, score: 93.852 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)
vg0405362835 C A -0.12 -0.06 -0.02 -0.02 -0.05 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0405362835 NA 2.35E-10 Grain_weight 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
vg0405362835 1.90E-08 4.24E-20 mr1035 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
vg0405362835 1.97E-09 2.19E-10 mr1035 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
vg0405362835 NA 4.03E-14 mr1062 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
vg0405362835 NA 9.90E-44 mr1136 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
vg0405362835 NA 2.71E-13 mr1149 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
vg0405362835 1.51E-06 5.46E-16 mr1626 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
vg0405362835 1.29E-08 6.65E-09 mr1626 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
vg0405362835 5.77E-09 2.87E-34 mr1631 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
vg0405362835 8.75E-10 1.28E-09 mr1631 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
vg0405362835 NA 3.71E-16 mr1035_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
vg0405362835 NA 9.14E-20 mr1167_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
vg0405362835 NA 7.40E-62 mr1402_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
vg0405362835 NA 1.37E-08 mr1489_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
vg0405362835 NA 3.25E-33 mr1631_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
vg0405362835 NA 2.62E-14 mr1726_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