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Detailed information for vg0212421980:

Variant ID: vg0212421980 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 12421980
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGCTAGGGTCTGGGTTAGTGCGGGCAGTTTAGCGAAAAAAACCCTCGAGTTTTAAGTTTTACAGCGCGGTCCTAACGCGCGTACTTTCCTTACTTATAAT[G/A]
TAATAATCGTCTTTTTGAAGGGACTCTACGGAAAATAACACCCCACAAGTACTATTCACGGGGGACTGCGGACGAATTACGCGTGAACCGGAGGGCTTTT

Reverse complement sequence

AAAAGCCCTCCGGTTCACGCGTAATTCGTCCGCAGTCCCCCGTGAATAGTACTTGTGGGGTGTTATTTTCCGTAGAGTCCCTTCAAAAAGACGATTATTA[C/T]
ATTATAAGTAAGGAAAGTACGCGCGTTAGGACCGCGCTGTAAAACTTAAAACTCGAGGGTTTTTTTCGCTAAACTGCCCGCACTAACCCAGACCCTAGCC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.90% 10.10% 1.06% 0.00% NA
All Indica  2759 99.10% 0.90% 0.04% 0.00% NA
All Japonica  1512 73.70% 23.10% 3.17% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.50% 0.30% 0.17% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 78.00% 17.70% 4.30% 0.00% NA
Tropical Japonica  504 81.50% 17.70% 0.79% 0.00% NA
Japonica Intermediate  241 44.00% 51.50% 4.56% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 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
vg0212421980 G -> A LOC_Os02g20980.2 upstream_gene_variant ; 553.0bp to feature; MODIFIER silent_mutation Average:99.738; most accessible tissue: Zhenshan97 panicle, score: 99.904 N N N N
vg0212421980 G -> A LOC_Os02g20980-LOC_Os02g20990 intergenic_region ; MODIFIER silent_mutation Average:99.738; most accessible tissue: Zhenshan97 panicle, score: 99.904 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)
vg0212421980 G A -0.03 -0.02 -0.01 -0.04 -0.03 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0212421980 4.72E-06 NA Awn_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
vg0212421980 1.48E-06 1.47E-06 mr1197_2 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