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Detailed information for vg1119227478:

Variant ID: vg1119227478 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 19227478
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.05, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


CCAGCGCCGGCACCTCGCCGGAGATCTTGTAGTCGAGGCCGCGCTCGCTCAGCTGCAGGGAGACTCTCTGGTGGGTCCCGGCTATGGTGGTCTGCGACGC[G/A]
GACAACATGTGGAAGATGGGGGGGTGTTCGACGGGGGCTCCCGGGTCGTCGTCGCCGTCGGTGCCCACGATGACAGCACCGGCGCCATCGCCGAACAGCG

Reverse complement sequence

CGCTGTTCGGCGATGGCGCCGGTGCTGTCATCGTGGGCACCGACGGCGACGACGACCCGGGAGCCCCCGTCGAACACCCCCCCATCTTCCACATGTTGTC[C/T]
GCGTCGCAGACCACCATAGCCGGGACCCACCAGAGAGTCTCCCTGCAGCTGAGCGAGCGCGGCCTCGACTACAAGATCTCCGGCGAGGTGCCGGCGCTGG

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 50.50% 49.40% 0.08% 0.00% NA
All Indica  2759 27.00% 72.90% 0.14% 0.00% NA
All Japonica  1512 94.60% 5.40% 0.00% 0.00% NA
Aus  269 32.00% 68.00% 0.00% 0.00% NA
Indica I  595 60.30% 39.70% 0.00% 0.00% NA
Indica II  465 9.00% 90.80% 0.22% 0.00% NA
Indica III  913 14.10% 85.50% 0.33% 0.00% NA
Indica Intermediate  786 27.40% 72.60% 0.00% 0.00% NA
Temperate Japonica  767 96.10% 3.90% 0.00% 0.00% NA
Tropical Japonica  504 96.60% 3.40% 0.00% 0.00% NA
Japonica Intermediate  241 85.90% 14.10% 0.00% 0.00% NA
VI/Aromatic  96 83.30% 16.70% 0.00% 0.00% NA
Intermediate  90 51.10% 48.90% 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
vg1119227478 G -> A LOC_Os11g32580.1 synonymous_variant ; p.Ser242Ser; LOW synonymous_codon Average:77.575; most accessible tissue: Minghui63 young leaf, score: 84.144 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)
vg1119227478 G A -0.03 -0.02 -0.02 -0.02 -0.02 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1119227478 NA 9.76E-08 mr1272 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
vg1119227478 NA 3.58E-07 mr1629 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
vg1119227478 4.43E-09 4.43E-09 mr1655 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
vg1119227478 9.22E-06 9.22E-06 mr1666 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
vg1119227478 NA 1.06E-07 mr1712 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
vg1119227478 9.51E-08 9.51E-08 mr1770 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
vg1119227478 NA 5.30E-07 mr1887 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
vg1119227478 NA 3.09E-10 mr1935 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