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Detailed information for vg0416372665:

Variant ID: vg0416372665 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 16372665
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCGTCGTATTTCTTTGCACCGGTGAGTTCGCGTCGTTGTCCTCTTCGTGTAGGTGCCTTCGGTTTAGCCGCCCGAGCTCTCTATCGTCGGCGGAGTCGTG[G/C]
TCCAGTGCCATGGCTGCGATGATGTCATCGATGACATCATAATTCCCTTCTAAATCTCTAAAAGCTTTTCTGTATTAGATGAAATCTGATTAAAACTTCG

Reverse complement sequence

CGAAGTTTTAATCAGATTTCATCTAATACAGAAAAGCTTTTAGAGATTTAGAAGGGAATTATGATGTCATCGATGACATCATCGCAGCCATGGCACTGGA[C/G]
CACGACTCCGCCGACGATAGAGAGCTCGGGCGGCTAAACCGAAGGCACCTACACGAAGAGGACAACGACGCGAACTCACCGGTGCAAAGAAATACGACGA

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 94.10% 3.60% 2.29% 0.00% NA
All Indica  2759 97.30% 0.20% 2.50% 0.00% NA
All Japonica  1512 86.80% 10.90% 2.31% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 92.10% 0.70% 7.23% 0.00% NA
Indica II  465 98.30% 0.00% 1.72% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 97.60% 0.10% 2.29% 0.00% NA
Temperate Japonica  767 80.60% 15.90% 3.52% 0.00% NA
Tropical Japonica  504 99.00% 0.80% 0.20% 0.00% NA
Japonica Intermediate  241 80.90% 16.20% 2.90% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 2.20% 3.33% 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
vg0416372665 G -> C LOC_Os04g27700.1 missense_variant ; p.Asp4Glu; MODERATE nonsynonymous_codon ; D4E Average:89.586; most accessible tissue: Zhenshan97 panicle, score: 97.226 unknown unknown TOLERATED 0.64

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)
vg0416372665 G C -0.11 -0.09 -0.09 -0.08 -0.1 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0416372665 3.19E-06 3.19E-06 mr1577 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