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Detailed information for vg0509425592:

Variant ID: vg0509425592 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 9425592
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGCTGGGCCTTGGCCTGCGGCCGGCCCAGCAAGGAGGAGGGGGAAGGAAAGGAGAGAATGGGCCGGCGGCCCATTCGAAAAAAAGGAGGAAAAAGGGAG[G/C]
AAAAAGAAAAAGAAAAAGGAAAAAGGATTTTCCCTGGAATTAAAATATTGCTTGCTCAATTTTAATTGGTTAAAATTATTTCTAGAGCTCTGAAAATTCC

Reverse complement sequence

GGAATTTTCAGAGCTCTAGAAATAATTTTAACCAATTAAAATTGAGCAAGCAATATTTTAATTCCAGGGAAAATCCTTTTTCCTTTTTCTTTTTCTTTTT[C/G]
CTCCCTTTTTCCTCCTTTTTTTCGAATGGGCCGCCGGCCCATTCTCTCCTTTCCTTCCCCCTCCTCCTTGCTGGGCCGGCCGCAGGCCAAGGCCCAGCCA

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 79.30% 1.60% 14.39% 4.72% NA
All Indica  2759 76.30% 0.00% 17.94% 5.76% NA
All Japonica  1512 92.20% 5.00% 2.71% 0.13% NA
Aus  269 29.40% 0.00% 48.33% 22.30% NA
Indica I  595 91.90% 0.00% 4.03% 4.03% NA
Indica II  465 74.60% 0.00% 15.70% 9.68% NA
Indica III  913 61.00% 0.00% 33.30% 5.70% NA
Indica Intermediate  786 83.20% 0.00% 11.96% 4.83% NA
Temperate Japonica  767 95.30% 1.30% 3.26% 0.13% NA
Tropical Japonica  504 90.50% 7.70% 1.59% 0.20% NA
Japonica Intermediate  241 85.90% 10.80% 3.32% 0.00% NA
VI/Aromatic  96 92.70% 0.00% 6.25% 1.04% NA
Intermediate  90 87.80% 2.20% 8.89% 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
vg0509425592 G -> DEL N N silent_mutation Average:59.285; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0509425592 G -> C LOC_Os05g16620.1 upstream_gene_variant ; 1818.0bp to feature; MODIFIER silent_mutation Average:59.285; most accessible tissue: Minghui63 panicle, score: 81.412 N N N N
vg0509425592 G -> C LOC_Os05g16620-LOC_Os05g16630 intergenic_region ; MODIFIER silent_mutation Average:59.285; most accessible tissue: Minghui63 panicle, score: 81.412 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)
vg0509425592 G C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0509425592 NA 1.62E-06 mr1693 Jap_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
vg0509425592 2.45E-06 NA mr1613_2 Jap_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
vg0509425592 4.96E-07 NA mr1962_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