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Detailed information for vg0222221990:

Variant ID: vg0222221990 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 22221990
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCTCATCTTCTCTGCCGCCATGCTGCCATCCCCCCTTCTTCTCCTCCAGATCTGAGGCGGGATAGCCTGGATCTTGCTGGCCCCCCTTCTTCTCCTCCAG[C/T]
GTGGCGCAGCGGTGGAGAAGGCTGGCACCGGCGAGGTGGCAGCCGACGCGGGCGAGGGTGCTGGTTGTGGGTTAAGAACCGGCACCTATAATCTCTATAG

Reverse complement sequence

CTATAGAGATTATAGGTGCCGGTTCTTAACCCACAACCAGCACCCTCGCCCGCGTCGGCTGCCACCTCGCCGGTGCCAGCCTTCTCCACCGCTGCGCCAC[G/A]
CTGGAGGAGAAGAAGGGGGGCCAGCAAGATCCAGGCTATCCCGCCTCAGATCTGGAGGAGAAGAAGGGGGGATGGCAGCATGGCGGCAGAGAAGATGAGA

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 78.30% 21.60% 0.11% 0.00% NA
All Indica  2759 94.30% 5.60% 0.11% 0.00% NA
All Japonica  1512 53.00% 47.00% 0.00% 0.00% NA
Aus  269 73.20% 26.40% 0.37% 0.00% NA
Indica I  595 90.10% 9.70% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 97.20% 2.70% 0.11% 0.00% NA
Indica Intermediate  786 91.00% 8.90% 0.13% 0.00% NA
Temperate Japonica  767 85.90% 14.10% 0.00% 0.00% NA
Tropical Japonica  504 17.70% 82.30% 0.00% 0.00% NA
Japonica Intermediate  241 22.40% 77.60% 0.00% 0.00% NA
VI/Aromatic  96 40.60% 59.40% 0.00% 0.00% NA
Intermediate  90 70.00% 28.90% 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
vg0222221990 C -> T LOC_Os02g36830.1 downstream_gene_variant ; 4039.0bp to feature; MODIFIER silent_mutation Average:79.881; most accessible tissue: Zhenshan97 young leaf, score: 90.547 N N N N
vg0222221990 C -> T LOC_Os02g36830-LOC_Os02g36840 intergenic_region ; MODIFIER silent_mutation Average:79.881; most accessible tissue: Zhenshan97 young leaf, score: 90.547 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)
vg0222221990 C T -0.01 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0222221990 NA 2.03E-07 Awn_length Ind_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
vg0222221990 NA 1.13E-06 mr1171 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
vg0222221990 NA 1.65E-06 mr1871 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
vg0222221990 NA 4.99E-06 mr1977 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
vg0222221990 NA 7.27E-10 mr1338_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
vg0222221990 NA 8.22E-06 mr1554_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
vg0222221990 1.78E-06 NA mr1739_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
vg0222221990 NA 4.38E-08 mr1871_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
vg0222221990 NA 3.39E-06 mr1908_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