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Detailed information for vg0529866867:

Variant ID: vg0529866867 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 29866867
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CTAATGGAAAACGAGCCTAATGCTCGGAACGGCTCCTGCGGTCGGTGGAGTCGAAGGCGTCCTCCTGCTCGTCACCCGGTCCCTCTGAGCGACTCCCGGA[G/A]
CCTGGCAGATAAGTCTCGCCGCTGCCTGACTGTGAGCCACTGGAGCTGCTGCTGAGATCGCGGCTGCCACTGGGAGTAGCAGACAACCAACCTCCGGTGC

Reverse complement sequence

GCACCGGAGGTTGGTTGTCTGCTACTCCCAGTGGCAGCCGCGATCTCAGCAGCAGCTCCAGTGGCTCACAGTCAGGCAGCGGCGAGACTTATCTGCCAGG[C/T]
TCCGGGAGTCGCTCAGAGGGACCGGGTGACGAGCAGGAGGACGCCTTCGACTCCACCGACCGCAGGAGCCGTTCCGAGCATTAGGCTCGTTTTCCATTAG

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 82.10% 0.10% 14.11% 3.64% NA
All Indica  2759 89.90% 0.00% 10.08% 0.00% NA
All Japonica  1512 64.60% 0.40% 23.88% 11.18% NA
Aus  269 94.80% 0.00% 5.20% 0.00% NA
Indica I  595 73.30% 0.00% 26.72% 0.00% NA
Indica II  465 92.30% 0.00% 7.74% 0.00% NA
Indica III  913 99.80% 0.00% 0.22% 0.00% NA
Indica Intermediate  786 89.70% 0.00% 10.31% 0.00% NA
Temperate Japonica  767 50.80% 0.40% 35.85% 12.91% NA
Tropical Japonica  504 84.50% 0.00% 7.14% 8.33% NA
Japonica Intermediate  241 66.40% 1.20% 20.75% 11.62% NA
VI/Aromatic  96 95.80% 0.00% 1.04% 3.12% NA
Intermediate  90 85.60% 0.00% 14.44% 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
vg0529866867 G -> DEL LOC_Os05g52010.1 N frameshift_variant Average:65.195; most accessible tissue: Zhenshan97 flag leaf, score: 89.88 N N N N
vg0529866867 G -> A LOC_Os05g52010.1 synonymous_variant ; p.Gly260Gly; LOW synonymous_codon Average:65.195; most accessible tissue: Zhenshan97 flag leaf, score: 89.88 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)
vg0529866867 G A -0.01 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0529866867 3.85E-06 NA mr1030_2 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