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Detailed information for vg0219166982:

Variant ID: vg0219166982 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 19166982
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGCTGCTACAGCAGCAGCTTGTTGTTGCTGCTGCGGCGGTGGGCGGCGGCGGCAACAACAACAACACGGCGGTGTTCAGTGACCTGCGAAGCGAGCTTAC[T/C]
TGTAGCCAGCGCCGCTTTGACGACTTCGGCGGCGGCTTCGTGCCGCGGAAGCGCGCGCGGGTTGGCGGCGAGGGAGAGGCGGCGGCGGGTCTGTTGATGA

Reverse complement sequence

TCATCAACAGACCCGCCGCCGCCTCTCCCTCGCCGCCAACCCGCGCGCGCTTCCGCGGCACGAAGCCGCCGCCGAAGTCGTCAAAGCGGCGCTGGCTACA[A/G]
GTAAGCTCGCTTCGCAGGTCACTGAACACCGCCGTGTTGTTGTTGTTGCCGCCGCCGCCCACCGCCGCAGCAGCAACAACAAGCTGCTGCTGTAGCAGCG

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 89.70% 10.20% 0.08% 0.00% NA
All Indica  2759 89.50% 10.30% 0.14% 0.00% NA
All Japonica  1512 89.30% 10.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.70% 1.30% 0.00% 0.00% NA
Indica III  913 76.50% 23.40% 0.11% 0.00% NA
Indica Intermediate  786 91.50% 8.10% 0.38% 0.00% NA
Temperate Japonica  767 96.30% 3.70% 0.00% 0.00% NA
Tropical Japonica  504 81.50% 18.50% 0.00% 0.00% NA
Japonica Intermediate  241 83.00% 17.00% 0.00% 0.00% NA
VI/Aromatic  96 76.00% 24.00% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 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
vg0219166982 T -> C LOC_Os02g32420.1 synonymous_variant ; p.Thr81Thr; LOW synonymous_codon Average:84.168; most accessible tissue: Zhenshan97 flower, score: 94.897 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)
vg0219166982 T C 0.02 0.02 0.01 0.01 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0219166982 1.77E-06 NA mr1107 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
vg0219166982 NA 1.49E-06 mr1213 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
vg0219166982 NA 8.85E-06 mr1224 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
vg0219166982 NA 1.51E-06 mr1248 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
vg0219166982 3.74E-06 NA mr1699 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