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Detailed information for vg0216185343:

Variant ID: vg0216185343 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 16185343
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGACCGCCACGTAGGCGCCACATCAGCGAAACCACCCTCCAAAACTGCCGAGGGAGTCAAATTACACCGGTTTTGAGAGTTAGGAGGTCGAGATATCCG[G/A]
TTTTATGGTTTAGGGTGACATATTAGATTTCGATCACTTTTAAGAGTCACAAAGTGAACTTATTCCTTTGTCCTCCCTTCATTTCATTCATGGGCCACAG

Reverse complement sequence

CTGTGGCCCATGAATGAAATGAAGGGAGGACAAAGGAATAAGTTCACTTTGTGACTCTTAAAAGTGATCGAAATCTAATATGTCACCCTAAACCATAAAA[C/T]
CGGATATCTCGACCTCCTAACTCTCAAAACCGGTGTAATTTGACTCCCTCGGCAGTTTTGGAGGGTGGTTTCGCTGATGTGGCGCCTACGTGGCGGTCTT

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 93.90% 6.10% 0.08% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 81.50% 18.30% 0.26% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 97.10% 2.70% 0.13% 0.00% NA
Tropical Japonica  504 55.80% 43.70% 0.60% 0.00% NA
Japonica Intermediate  241 85.50% 14.50% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 92.20% 7.80% 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
vg0216185343 G -> A LOC_Os02g27450.1 upstream_gene_variant ; 530.0bp to feature; MODIFIER silent_mutation Average:88.429; most accessible tissue: Minghui63 root, score: 96.187 N N N N
vg0216185343 G -> A LOC_Os02g27450-LOC_Os02g27460 intergenic_region ; MODIFIER silent_mutation Average:88.429; most accessible tissue: Minghui63 root, score: 96.187 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)
vg0216185343 G A -0.01 -0.01 -0.01 -0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0216185343 NA 6.91E-07 mr1422 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
vg0216185343 NA 2.82E-06 mr1583 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
vg0216185343 1.26E-06 3.62E-08 mr1042_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
vg0216185343 6.04E-06 8.34E-09 mr1742_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
vg0216185343 3.03E-08 3.85E-09 mr1871_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