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Detailed information for vg0521505292:

Variant ID: vg0521505292 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 21505292
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCCGCACGCACAGCGCGGTGCGCCGGATGCTCGCAGCTCGCGTGCTCGCCCCCTGTAGCGCGGTGGCCTCAGACCAGGGTACCTTTTCCGTTTTCAACA[C/T]
AAAAACCGACTCTCACGGGTTTATCGGAAACATGTAGAAGAAAAAAAGCCGACTTTCGTTCAACACCGTATAGATACAGGTTGAAACTGATTGATTTTCA

Reverse complement sequence

TGAAAATCAATCAGTTTCAACCTGTATCTATACGGTGTTGAACGAAAGTCGGCTTTTTTTCTTCTACATGTTTCCGATAAACCCGTGAGAGTCGGTTTTT[G/A]
TGTTGAAAACGGAAAAGGTACCCTGGTCTGAGGCCACCGCGCTACAGGGGGCGAGCACGCGAGCTGCGAGCATCCGGCGCACCGCGCTGTGCGTGCGGCG

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 84.50% 14.00% 1.50% 0.00% NA
All Indica  2759 99.30% 0.50% 0.14% 0.00% NA
All Japonica  1512 54.00% 41.60% 4.43% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.30% 0.00% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.00% 0.60% 0.38% 0.00% NA
Temperate Japonica  767 22.00% 72.40% 5.61% 0.00% NA
Tropical Japonica  504 94.60% 3.20% 2.18% 0.00% NA
Japonica Intermediate  241 70.50% 24.10% 5.39% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0521505292 C -> T LOC_Os05g36290.1 upstream_gene_variant ; 1044.0bp to feature; MODIFIER silent_mutation Average:95.833; most accessible tissue: Zhenshan97 flower, score: 99.57 N N N N
vg0521505292 C -> T LOC_Os05g36290.2 upstream_gene_variant ; 1044.0bp to feature; MODIFIER silent_mutation Average:95.833; most accessible tissue: Zhenshan97 flower, score: 99.57 N N N N
vg0521505292 C -> T LOC_Os05g36300.1 downstream_gene_variant ; 2983.0bp to feature; MODIFIER silent_mutation Average:95.833; most accessible tissue: Zhenshan97 flower, score: 99.57 N N N N
vg0521505292 C -> T LOC_Os05g36310.1 downstream_gene_variant ; 4090.0bp to feature; MODIFIER silent_mutation Average:95.833; most accessible tissue: Zhenshan97 flower, score: 99.57 N N N N
vg0521505292 C -> T LOC_Os05g36290-LOC_Os05g36300 intergenic_region ; MODIFIER silent_mutation Average:95.833; most accessible tissue: Zhenshan97 flower, score: 99.57 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)
vg0521505292 C T 0.01 0.0 0.0 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0521505292 NA 3.45E-36 Grain_thickness All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0521505292 NA 1.77E-13 Grain_thickness Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0521505292 8.59E-06 NA mr1071 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
vg0521505292 5.86E-06 NA mr1080 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
vg0521505292 NA 1.70E-06 mr1087 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
vg0521505292 NA 7.01E-31 mr1137 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
vg0521505292 NA 2.81E-09 mr1137 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
vg0521505292 9.12E-07 NA mr1140 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
vg0521505292 NA 2.36E-12 mr1182 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
vg0521505292 NA 9.47E-10 mr1282 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
vg0521505292 NA 3.45E-07 mr1617 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
vg0521505292 NA 1.69E-06 mr1629 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
vg0521505292 NA 1.01E-11 mr1650 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
vg0521505292 NA 1.04E-08 mr1658 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
vg0521505292 NA 5.14E-06 mr1708 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
vg0521505292 NA 2.88E-12 mr1712 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
vg0521505292 NA 1.95E-07 mr1763 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
vg0521505292 NA 1.89E-12 mr1844 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
vg0521505292 NA 6.02E-09 mr1880 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
vg0521505292 NA 1.04E-09 mr1880 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
vg0521505292 NA 3.01E-08 mr1977 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
vg0521505292 NA 1.06E-13 mr1182_2 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
vg0521505292 NA 1.38E-07 mr1748_2 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
vg0521505292 NA 2.62E-07 mr1880_2 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