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Detailed information for vg1126213378:

Variant ID: vg1126213378 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26213378
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


CGCCCGCGACTGCCAGGACTGCGTCGAGCAGTACGCGCAGTGCATCGCAGCTGGGCCATCCTCCAAGAGCCTCCTCCTCGGCCGCCTCCGCCGGGTGTCC[C/T]
GGCTTGTCCGGAGCCTCCCCGAACGCCACAGGCTGGCCGTGCAGATCCAAGACATCAAGGTCCGGCTGGGCGAGGTGAGCCACCGGCGGAAGGCGTATGA

Reverse complement sequence

TCATACGCCTTCCGCCGGTGGCTCACCTCGCCCAGCCGGACCTTGATGTCTTGGATCTGCACGGCCAGCCTGTGGCGTTCGGGGAGGCTCCGGACAAGCC[G/A]
GGACACCCGGCGGAGGCGGCCGAGGAGGAGGCTCTTGGAGGATGGCCCAGCTGCGATGCACTGCGCGTACTGCTCGACGCAGTCCTGGCAGTCGCGGGCG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 76.90% 20.50% 0.13% 2.48% NA
All Indica  2759 71.10% 28.80% 0.11% 0.04% NA
All Japonica  1512 88.00% 4.50% 0.20% 7.34% NA
Aus  269 64.30% 34.20% 0.00% 1.49% NA
Indica I  595 96.10% 3.90% 0.00% 0.00% NA
Indica II  465 66.50% 33.30% 0.22% 0.00% NA
Indica III  913 63.40% 36.60% 0.00% 0.00% NA
Indica Intermediate  786 63.70% 35.90% 0.25% 0.13% NA
Temperate Japonica  767 98.30% 1.00% 0.13% 0.52% NA
Tropical Japonica  504 77.20% 10.70% 0.40% 11.71% NA
Japonica Intermediate  241 77.60% 2.50% 0.00% 19.92% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 84.40% 14.40% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126213378 C -> T LOC_Os11g43410.1 missense_variant ; p.Arg115Trp; MODERATE nonsynonymous_codon ; R115W Average:80.393; most accessible tissue: Zhenshan97 young leaf, score: 92.102 unknown unknown TOLERATED 0.07
vg1126213378 C -> DEL LOC_Os11g43410.1 N frameshift_variant Average:80.393; most accessible tissue: Zhenshan97 young leaf, score: 92.102 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)
vg1126213378 C T 0.0 -0.01 -0.01 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126213378 1.95E-06 1.95E-06 mr1540 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
vg1126213378 1.54E-06 1.65E-07 mr1732 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
vg1126213378 NA 8.92E-06 mr1133_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