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Detailed information for vg0719886670:

Variant ID: vg0719886670 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 19886670
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTTTATCTCTTTAAACGTATGTTAAAATACTATATTTACGGATTTGTGTGTATGAAGGTGTACGTGTATATATGTCATGTACTACCCCGTTTTATTA[T/C]
AAGTGCCGCTGTCGATTTTCGTGTAAAATATTTTAAAAAATAGTCACACACAAAGTATTATTTATATTTTTATTATTTAATAATAATAAAAATACTAAAC

Reverse complement sequence

GTTTAGTATTTTTATTATTATTAAATAATAAAAATATAAATAATACTTTGTGTGTGACTATTTTTTAAAATATTTTACACGAAAATCGACAGCGGCACTT[A/G]
TAATAAAACGGGGTAGTACATGACATATATACACGTACACCTTCATACACACAAATCCGTAAATATAGTATTTTAACATACGTTTAAAGAGATAAAAACC

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 93.00% 6.90% 0.13% 0.00% NA
All Indica  2759 99.50% 0.50% 0.04% 0.00% NA
All Japonica  1512 79.30% 20.40% 0.33% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.10% 0.90% 0.00% 0.00% NA
Indica Intermediate  786 99.10% 0.80% 0.13% 0.00% NA
Temperate Japonica  767 60.00% 39.40% 0.65% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0719886670 T -> C LOC_Os07g33270.1 downstream_gene_variant ; 507.0bp to feature; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 root, score: 97.791 N N N N
vg0719886670 T -> C LOC_Os07g33260-LOC_Os07g33270 intergenic_region ; MODIFIER silent_mutation Average:85.923; most accessible tissue: Minghui63 root, score: 97.791 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)
vg0719886670 T C -0.03 0.01 0.0 0.0 0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0719886670 1.59E-08 NA Heading_date All YES 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
vg0719886670 1.41E-06 NA Plant_height 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
vg0719886670 2.16E-06 NA Spikelet_length 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