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Detailed information for vg1124963624:

Variant ID: vg1124963624 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24963624
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.83, C: 0.18, others allele: 0.00, population size: 263. )

Flanking Sequence (100 bp) in Reference Genome:


CACCTAACTCGAGGTCAACATCAATATATAAGGCCACACACACTCATGTGTCCAATGTAACTAGCGTCTCGAGTGTGAGTAGCACAAGGCAAGGCGGAAC[T/C]
GCCACCCTCAAGCTTAAGTTCAAAGAATATGGTCTGGCTCTGCAAGGGAGAGAGGAAGAAATAGGTCCAAATTAAGTTAAACATGTAGATATACTTGACC

Reverse complement sequence

GGTCAAGTATATCTACATGTTTAACTTAATTTGGACCTATTTCTTCCTCTCTCCCTTGCAGAGCCAGACCATATTCTTTGAACTTAAGCTTGAGGGTGGC[A/G]
GTTCCGCCTTGCCTTGTGCTACTCACACTCGAGACGCTAGTTACATTGGACACATGAGTGTGTGTGGCCTTATATATTGATGTTGACCTCGAGTTAGGTG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.30% 8.60% 0.04% 0.00% NA
All Indica  2759 94.80% 5.10% 0.04% 0.00% NA
All Japonica  1512 93.50% 6.40% 0.07% 0.00% NA
Aus  269 58.70% 41.30% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 88.80% 11.20% 0.00% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 92.20% 7.60% 0.13% 0.00% NA
Temperate Japonica  767 97.90% 2.10% 0.00% 0.00% NA
Tropical Japonica  504 94.40% 5.60% 0.00% 0.00% NA
Japonica Intermediate  241 77.60% 22.00% 0.41% 0.00% NA
VI/Aromatic  96 55.20% 44.80% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1124963624 T -> C LOC_Os11g41600-LOC_Os11g41610 intergenic_region ; MODIFIER silent_mutation Average:81.097; most accessible tissue: Callus, score: 96.601 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)
vg1124963624 T C -0.2 -0.08 -0.03 -0.01 -0.1 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124963624 2.46E-07 NA mr1609 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
vg1124963624 3.45E-07 NA mr1841 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
vg1124963624 4.55E-06 NA mr1945 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
vg1124963624 1.46E-06 NA mr1609_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
vg1124963624 1.34E-06 NA mr1841_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
vg1124963624 2.50E-06 NA mr1900_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