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Detailed information for vg0134573656:

Variant ID: vg0134573656 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 34573656
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATATCAACCCCACGTAGGCGTCATGTCAGTCGAAACTGTCGTTCAAACCACCTTGGAATCTTATTTGCACTGGTTTTGGGAGTTGAGGGACACATCATAT[C/T]
TGTTATTGTGGTTCATGACGAATTTCGGACTCGGTGACAATTTTGAGGGACCTAATGTGAACTTATTCCTCCCGGGAAAAAAACGAGCCCAATAGGCGTG

Reverse complement sequence

CACGCCTATTGGGCTCGTTTTTTTCCCGGGAGGAATAAGTTCACATTAGGTCCCTCAAAATTGTCACCGAGTCCGAAATTCGTCATGAACCACAATAACA[G/A]
ATATGATGTGTCCCTCAACTCCCAAAACCAGTGCAAATAAGATTCCAAGGTGGTTTGAACGACAGTTTCGACTGACATGACGCCTACGTGGGGTTGATAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.70% 11.30% 0.00% 0.00% NA
All Indica  2759 90.80% 9.20% 0.00% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 2.20% 97.80% 0.00% 0.00% NA
Indica I  595 97.10% 2.90% 0.00% 0.00% NA
Indica II  465 80.90% 19.10% 0.00% 0.00% NA
Indica III  913 92.30% 7.70% 0.00% 0.00% NA
Indica Intermediate  786 89.90% 10.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 88.90% 11.10% 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
vg0134573656 C -> T LOC_Os01g59780.1 upstream_gene_variant ; 1176.0bp to feature; MODIFIER silent_mutation Average:91.616; most accessible tissue: Minghui63 young leaf, score: 95.637 N N N N
vg0134573656 C -> T LOC_Os01g59770.1 downstream_gene_variant ; 3236.0bp to feature; MODIFIER silent_mutation Average:91.616; most accessible tissue: Minghui63 young leaf, score: 95.637 N N N N
vg0134573656 C -> T LOC_Os01g59770-LOC_Os01g59780 intergenic_region ; MODIFIER silent_mutation Average:91.616; most accessible tissue: Minghui63 young leaf, score: 95.637 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)
vg0134573656 C T -0.06 -0.06 -0.05 -0.06 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0134573656 NA 7.76E-10 mr1193 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
vg0134573656 NA 1.16E-10 mr1232 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
vg0134573656 NA 9.62E-11 mr1471 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
vg0134573656 NA 4.65E-10 mr1722 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
vg0134573656 NA 1.84E-16 mr1193_2 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