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Detailed information for vg0404543398:

Variant ID: vg0404543398 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 4543398
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATCTGCCTTCTTCTTTTTTTTTTCTTTTGCCCCTATCTTGTCGTTTAGGAAACATCCCCACAAACCACCATTGTTTGAGTCACAGTCACTGACTTCTGGT[C/A]
CCACCTACTTCTGCGACCTAACTGGCCCCACGCGTCAGTCTCTCTACTCATGATCCTGCTTGGTACACCACCGATTTATTATATTTGGGTCCAGGCAACC

Reverse complement sequence

GGTTGCCTGGACCCAAATATAATAAATCGGTGGTGTACCAAGCAGGATCATGAGTAGAGAGACTGACGCGTGGGGCCAGTTAGGTCGCAGAAGTAGGTGG[G/T]
ACCAGAAGTCAGTGACTGTGACTCAAACAATGGTGGTTTGTGGGGATGTTTCCTAAACGACAAGATAGGGGCAAAAGAAAAAAAAAAGAAGAAGGCAGAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.10% 15.90% 0.00% 0.00% NA
All Indica  2759 80.00% 20.00% 0.00% 0.00% NA
All Japonica  1512 89.50% 10.50% 0.00% 0.00% NA
Aus  269 87.70% 12.30% 0.00% 0.00% NA
Indica I  595 92.90% 7.10% 0.00% 0.00% NA
Indica II  465 94.60% 5.40% 0.00% 0.00% NA
Indica III  913 65.30% 34.70% 0.00% 0.00% NA
Indica Intermediate  786 78.60% 21.40% 0.00% 0.00% NA
Temperate Japonica  767 99.00% 1.00% 0.00% 0.00% NA
Tropical Japonica  504 81.00% 19.00% 0.00% 0.00% NA
Japonica Intermediate  241 77.20% 22.80% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0404543398 C -> A LOC_Os04g08440.1 upstream_gene_variant ; 4182.0bp to feature; MODIFIER silent_mutation Average:99.442; most accessible tissue: Minghui63 young leaf, score: 99.752 N N N N
vg0404543398 C -> A LOC_Os04g08450.3 upstream_gene_variant ; 219.0bp to feature; MODIFIER silent_mutation Average:99.442; most accessible tissue: Minghui63 young leaf, score: 99.752 N N N N
vg0404543398 C -> A LOC_Os04g08450.1 upstream_gene_variant ; 219.0bp to feature; MODIFIER silent_mutation Average:99.442; most accessible tissue: Minghui63 young leaf, score: 99.752 N N N N
vg0404543398 C -> A LOC_Os04g08450.2 upstream_gene_variant ; 219.0bp to feature; MODIFIER silent_mutation Average:99.442; most accessible tissue: Minghui63 young leaf, score: 99.752 N N N N
vg0404543398 C -> A LOC_Os04g08440-LOC_Os04g08450 intergenic_region ; MODIFIER silent_mutation Average:99.442; most accessible tissue: Minghui63 young leaf, score: 99.752 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)
vg0404543398 C A -0.17 -0.26 -0.2 -0.19 -0.12 -0.15

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0404543398 6.39E-07 6.51E-07 mr1136_2 Ind_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
vg0404543398 NA 1.76E-06 mr1595_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
vg0404543398 NA 4.03E-09 mr1798_2 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