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Detailed information for vg1126921542:

Variant ID: vg1126921542 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 26921542
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTGGTCGGCGCAGACGTCGGCAGGCTCATCTCCATGATCATGCAGGCGGCGTTGCCGGCTCAGCGGAACAAGAAGGAGTGCGAGCAGCTCGCCCGCCG[T/C]
GTGTTCATGATCGCCGAGCTGCTGCCGCACCTGCAGGACCCGGAGGTGATGCGGCGGCCGGAGGTCCGGCGGTCGCTGGCCGGGCTCGGCGACACGCTCC

Reverse complement sequence

GGAGCGTGTCGCCGAGCCCGGCCAGCGACCGCCGGACCTCCGGCCGCCGCATCACCTCCGGGTCCTGCAGGTGCGGCAGCAGCTCGGCGATCATGAACAC[A/G]
CGGCGGGCGAGCTGCTCGCACTCCTTCTTGTTCCGCTGAGCCGGCAACGCCGCCTGCATGATCATGGAGATGAGCCTGCCGACGTCTGCGCCGACCAGCT

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 75.90% 9.80% 0.47% 13.90% NA
All Indica  2759 66.30% 14.10% 0.54% 19.03% NA
All Japonica  1512 90.40% 2.60% 0.33% 6.68% NA
Aus  269 82.90% 8.90% 0.00% 8.18% NA
Indica I  595 48.70% 17.80% 0.34% 33.11% NA
Indica II  465 86.50% 10.30% 0.22% 3.01% NA
Indica III  913 61.60% 14.00% 0.88% 23.55% NA
Indica Intermediate  786 73.20% 13.70% 0.51% 12.60% NA
Temperate Japonica  767 91.00% 1.00% 0.52% 7.43% NA
Tropical Japonica  504 93.70% 1.40% 0.00% 4.96% NA
Japonica Intermediate  241 81.70% 10.00% 0.41% 7.88% NA
VI/Aromatic  96 93.80% 4.20% 1.04% 1.04% NA
Intermediate  90 84.40% 5.60% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1126921542 T -> DEL LOC_Os11g44510.1 N splice_donor_variant Average:67.749; most accessible tissue: Minghui63 root, score: 91.589 N N N N
vg1126921542 T -> C LOC_Os11g44510.1 splice_donor_variant&intron_variant ; HIGH splice_donor_variant Average:67.749; most accessible tissue: Minghui63 root, score: 91.589 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)
vg1126921542 T C -0.04 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1126921542 NA 7.34E-07 mr1553_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