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Detailed information for vg0124857371:

Variant ID: vg0124857371 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 24857371
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:


GCCCCGTCTGCGGCGCGTTCACCAGCGCCGCCGACGACGACGAGTCCGGCACCACCACCGTGAACTCCCCCCTGCACACCGCAACCAGCACCGCCACGAC[G/C]
GCCACCACCACCGTCGCCGCCGCCGTCGCGGAGAGCGCAGAGGCCACCATATCACCTTGCACGCTCGTGCGACGCGATGCGCTCGGAAGGGTCACGACCG

Reverse complement sequence

CGGTCGTGACCCTTCCGAGCGCATCGCGTCGCACGAGCGTGCAAGGTGATATGGTGGCCTCTGCGCTCTCCGCGACGGCGGCGGCGACGGTGGTGGTGGC[C/G]
GTCGTGGCGGTGCTGGTTGCGGTGTGCAGGGGGGAGTTCACGGTGGTGGTGCCGGACTCGTCGTCGTCGGCGGCGCTGGTGAACGCGCCGCAGACGGGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 68.90% 30.30% 0.40% 0.40% NA
All Indica  2759 47.80% 50.90% 0.65% 0.69% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 65.20% 34.10% 0.00% 0.67% NA
Indica II  465 55.10% 42.20% 1.29% 1.51% NA
Indica III  913 38.40% 60.70% 0.44% 0.44% NA
Indica Intermediate  786 41.20% 57.30% 1.02% 0.51% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 81.10% 17.80% 1.11% 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
vg0124857371 G -> DEL LOC_Os01g43440.1 N frameshift_variant Average:89.776; most accessible tissue: Minghui63 panicle, score: 96.113 N N N N
vg0124857371 G -> C LOC_Os01g43440.1 synonymous_variant ; p.Ala17Ala; LOW nonsynonymous_codon ; A17V Average:89.776; most accessible tissue: Minghui63 panicle, score: 96.113 unknown unknown TOLERATED 0.92

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)
vg0124857371 G C -0.01 -0.01 0.0 -0.01 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0124857371 NA 1.42E-08 mr1751_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
vg0124857371 NA 2.03E-06 mr1951_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