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Detailed information for vg0500578306:

Variant ID: vg0500578306 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 578306
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCTTTGCATCATAGTTCTGAAAATACAGTCTGTCTATCAGATCACCAGTTAAGCTATCTTGTGAACACAAAGGATAATAGTTCTGAGGACTCCGTACC[G/A]
CATCCAAAAGGACATTAGAGGTCTTGAAATCACGGTAGATGACTTTAACCTTGTCACTGTGGAGAAATGCGAGCCCTTTTGCTGCTCCAAGGGCAATTTT

Reverse complement sequence

AAAATTGCCCTTGGAGCAGCAAAAGGGCTCGCATTTCTCCACAGTGACAAGGTTAAAGTCATCTACCGTGATTTCAAGACCTCTAATGTCCTTTTGGATG[C/T]
GGTACGGAGTCCTCAGAACTATTATCCTTTGTGTTCACAAGATAGCTTAACTGGTGATCTGATAGACAGACTGTATTTTCAGAACTATGATGCAAAGCTC

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 69.80% 30.20% 0.04% 0.00% NA
All Indica  2759 55.60% 44.30% 0.07% 0.00% NA
All Japonica  1512 92.30% 7.70% 0.00% 0.00% NA
Aus  269 85.50% 14.50% 0.00% 0.00% NA
Indica I  595 30.90% 68.70% 0.34% 0.00% NA
Indica II  465 51.40% 48.60% 0.00% 0.00% NA
Indica III  913 72.80% 27.20% 0.00% 0.00% NA
Indica Intermediate  786 56.90% 43.10% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 80.40% 19.60% 0.00% 0.00% NA
Japonica Intermediate  241 93.40% 6.60% 0.00% 0.00% NA
VI/Aromatic  96 70.80% 29.20% 0.00% 0.00% NA
Intermediate  90 77.80% 22.20% 0.00% 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
vg0500578306 G -> A LOC_Os05g02020.1 missense_variant&splice_region_variant ; p.Ala215Val; MODERATE nonsynonymous_codon ; A215V Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown DELETERIOUS 0.03
vg0500578306 G -> A LOC_Os05g02020.2 missense_variant&splice_region_variant ; p.Ala213Val; MODERATE nonsynonymous_codon ; A213V Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 unknown unknown DELETERIOUS 0.03

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)
vg0500578306 G A -0.02 -0.03 -0.02 -0.02 -0.02 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500578306 NA 2.57E-06 mr1751 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
vg0500578306 NA 3.64E-06 mr1890 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
vg0500578306 NA 1.33E-08 mr1946 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
vg0500578306 8.73E-06 8.72E-06 mr1427_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
vg0500578306 NA 2.18E-06 mr1738_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