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Detailed information for vg1128795148:

Variant ID: vg1128795148 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 28795148
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.08, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTTATACTCTCGACTATTAGCTAACTTATATAGGGTCTTCAAAACAAATTCCTTGCAACTTCTCTCAAGTTACTTAATCACCTTTTAACTGTCATCAA[G/T]
TCACACCTCAGTCACGCGATTAGCTTTAGTTAGTTCATAATGCAAAATTCCTTGCAATTTTTGACAAGTCTTCTTGAGTCCTTTTGAGCTGTCCTTTTAG

Reverse complement sequence

CTAAAAGGACAGCTCAAAAGGACTCAAGAAGACTTGTCAAAAATTGCAAGGAATTTTGCATTATGAACTAACTAAAGCTAATCGCGTGACTGAGGTGTGA[C/A]
TTGATGACAGTTAAAAGGTGATTAAGTAACTTGAGAGAAGTTGCAAGGAATTTGTTTTGAAGACCCTATATAAGTTAGCTAATAGTCGAGAGTATAAAGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.10% 18.70% 0.25% 0.00% NA
All Indica  2759 90.30% 9.60% 0.07% 0.00% NA
All Japonica  1512 62.20% 37.20% 0.66% 0.00% NA
Aus  269 94.40% 5.60% 0.00% 0.00% NA
Indica I  595 90.40% 9.60% 0.00% 0.00% NA
Indica II  465 98.90% 1.10% 0.00% 0.00% NA
Indica III  913 87.80% 12.20% 0.00% 0.00% NA
Indica Intermediate  786 87.90% 11.80% 0.25% 0.00% NA
Temperate Japonica  767 80.20% 18.50% 1.30% 0.00% NA
Tropical Japonica  504 31.20% 68.80% 0.00% 0.00% NA
Japonica Intermediate  241 69.70% 30.30% 0.00% 0.00% NA
VI/Aromatic  96 72.90% 27.10% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1128795148 G -> T LOC_Os11g47730.1 downstream_gene_variant ; 314.0bp to feature; MODIFIER silent_mutation Average:86.683; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg1128795148 G -> T LOC_Os11g47730.2 downstream_gene_variant ; 314.0bp to feature; MODIFIER silent_mutation Average:86.683; most accessible tissue: Zhenshan97 panicle, score: 96.13 N N N N
vg1128795148 G -> T LOC_Os11g47730-LOC_Os11g47740 intergenic_region ; MODIFIER silent_mutation Average:86.683; most accessible tissue: Zhenshan97 panicle, score: 96.13 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)
vg1128795148 G T -0.18 -0.09 -0.07 0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1128795148 7.39E-06 NA mr1261 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
vg1128795148 1.96E-06 1.96E-06 mr1261 Jap_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
vg1128795148 1.30E-06 NA mr1310 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
vg1128795148 NA 5.80E-08 mr1310 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
vg1128795148 NA 6.16E-06 mr1546 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
vg1128795148 NA 8.25E-08 mr1800 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
vg1128795148 NA 2.20E-08 mr1805 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
vg1128795148 NA 1.37E-08 mr1862 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
vg1128795148 9.26E-08 9.25E-08 mr1899 Jap_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
vg1128795148 2.31E-06 NA mr1926 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
vg1128795148 NA 9.27E-09 mr1926 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
vg1128795148 NA 1.60E-06 mr1942 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