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Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0528741746:

Variant ID: vg0528741746 (JBrowse)Variation Type: INDEL
Chromosome: chr05Position: 28741746
Reference Allele: CAlternative Allele: T,CCTCT
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.72, T: 0.28, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


AGAAATGCATGGGAGGCAAGGCTCTGCAATCTGTGCCATCGGTTGCCTCGGGATGACAAATAAAATGCGACTAGCCATTGCGTGCCTAGCCTACCTCCTC[C/T,CCTCT]
CCTCTCGTCTTCCCCACAAGCCCACAAGAGAGGGACCGCATCTCATCTCATGTCCTTGCTCGTTTTTCAGACTTTCAATCACTGCATACTCCAACCTCAA

Reverse complement sequence

TTGAGGTTGGAGTATGCAGTGATTGAAAGTCTGAAAAACGAGCAAGGACATGAGATGAGATGCGGTCCCTCTCTTGTGGGCTTGTGGGGAAGACGAGAGG[G/A,AGAGG]
GAGGAGGTAGGCTAGGCACGCAATGGCTAGTCGCATTTTATTTGTCATCCCGAGGCAACCGATGGCACAGATTGCAGAGCCTTGCCTCCCATGCATTTCT

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 98.30% 1.60% 0.04% 0.00% CCTCT: 0.04%
All Indica  2759 97.40% 2.50% 0.04% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.00% 0.00% CCTCT: 0.07%
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 95.50% 4.50% 0.00% 0.00% NA
Indica II  465 96.80% 3.20% 0.00% 0.00% NA
Indica III  913 99.30% 0.50% 0.11% 0.00% NA
Indica Intermediate  786 97.10% 2.90% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.00% CCTCT: 0.41%
VI/Aromatic  96 95.80% 3.10% 0.00% 0.00% CCTCT: 1.04%
Intermediate  90 94.40% 4.40% 1.11% 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
vg0528741746 C -> T LOC_Os05g50140.1 upstream_gene_variant ; 3817.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> T LOC_Os05g50150.1 upstream_gene_variant ; 2099.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> T LOC_Os05g50140.2 upstream_gene_variant ; 3817.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> T LOC_Os05g50160.1 downstream_gene_variant ; 1629.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> T LOC_Os05g50170.1 downstream_gene_variant ; 3543.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> T LOC_Os05g50150-LOC_Os05g50160 intergenic_region ; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50140.1 upstream_gene_variant ; 3818.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50150.1 upstream_gene_variant ; 2100.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50140.2 upstream_gene_variant ; 3818.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50160.1 downstream_gene_variant ; 1628.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50170.1 downstream_gene_variant ; 3542.0bp to feature; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 N N N N
vg0528741746 C -> CCTCT LOC_Os05g50150-LOC_Os05g50160 intergenic_region ; MODIFIER silent_mutation Average:87.614; most accessible tissue: Callus, score: 99.786 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)
vg0528741746 C CCTCT -0.21 -0.07 -0.04 -0.13 -0.02 0.06
vg0528741746 C T -0.02 -0.04 -0.03 -0.05 -0.03 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0528741746 4.33E-06 NA mr1128 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
vg0528741746 NA 9.97E-06 mr1409 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