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Detailed information for vg0431879764:

Variant ID: vg0431879764 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31879764
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.90, G: 0.10, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:


GCGGCGATGGGAAGGGGATGATGAAGGAAGTTGGTGAGGACACCTCAGACTCACAGTTCGATGGCTACTTTCTCAGTTACTCCCCCGTTTCAAAACGTAA[G/A]
TCATTTATTTTTCATATTTATAGTAATACTAATAAATCTAAATAAAATTAATATTTTTTTATCTAGATTAATTAGTATCAATATAAATATGGAAAATGCT

Reverse complement sequence

AGCATTTTCCATATTTATATTGATACTAATTAATCTAGATAAAAAAATATTAATTTTATTTAGATTTATTAGTATTACTATAAATATGAAAAATAAATGA[C/T]
TTACGTTTTGAAACGGGGGAGTAACTGAGAAAGTAGCCATCGAACTGTGAGTCTGAGGTGTCCTCACCAACTTCCTTCATCATCCCCTTCCCATCGCCGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 32.10% 25.30% 9.06% 33.45% NA
All Indica  2759 25.70% 35.60% 13.41% 25.30% NA
All Japonica  1512 50.30% 5.30% 1.12% 43.32% NA
Aus  269 5.60% 21.90% 12.27% 60.22% NA
Indica I  595 22.70% 33.30% 14.45% 29.58% NA
Indica II  465 24.10% 51.00% 6.24% 18.71% NA
Indica III  913 25.10% 27.90% 17.63% 29.35% NA
Indica Intermediate  786 29.60% 37.20% 11.96% 21.25% NA
Temperate Japonica  767 80.20% 2.30% 1.69% 15.78% NA
Tropical Japonica  504 13.10% 9.50% 0.20% 77.18% NA
Japonica Intermediate  241 32.80% 5.80% 1.24% 60.17% NA
VI/Aromatic  96 3.10% 61.50% 0.00% 35.42% NA
Intermediate  90 35.60% 20.00% 8.89% 35.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0431879764 G -> DEL N N silent_mutation Average:90.612; most accessible tissue: Callus, score: 96.971 N N N N
vg0431879764 G -> A LOC_Os04g53510.1 upstream_gene_variant ; 15.0bp to feature; MODIFIER silent_mutation Average:90.612; most accessible tissue: Callus, score: 96.971 N N N N
vg0431879764 G -> A LOC_Os04g53520.1 downstream_gene_variant ; 729.0bp to feature; MODIFIER silent_mutation Average:90.612; most accessible tissue: Callus, score: 96.971 N N N N
vg0431879764 G -> A LOC_Os04g53510-LOC_Os04g53520 intergenic_region ; MODIFIER silent_mutation Average:90.612; most accessible tissue: Callus, score: 96.971 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)
vg0431879764 G A -0.04 -0.03 -0.01 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431879764 NA 7.91E-11 Heading_date Jap_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
vg0431879764 NA 1.37E-11 Plant_height Jap_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
vg0431879764 NA 3.82E-11 Spikelet_length Jap_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
vg0431879764 NA 5.81E-06 mr1003 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
vg0431879764 NA 1.24E-07 mr1010_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
vg0431879764 5.03E-06 NA 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
vg0431879764 NA 1.16E-07 mr1051_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
vg0431879764 NA 1.17E-07 mr1137_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
vg0431879764 NA 5.12E-06 mr1164_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
vg0431879764 NA 3.34E-07 mr1212_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
vg0431879764 NA 2.09E-08 mr1229_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
vg0431879764 NA 1.08E-07 mr1229_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
vg0431879764 3.36E-06 NA mr1241_2 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
vg0431879764 NA 1.26E-07 mr1521_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
vg0431879764 NA 2.03E-06 mr1555_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
vg0431879764 NA 8.62E-06 mr1596_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
vg0431879764 NA 4.52E-06 mr1617_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
vg0431879764 NA 3.65E-06 mr1763_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
vg0431879764 NA 6.93E-09 mr1880_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
vg0431879764 NA 6.59E-09 mr1880_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