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Detailed information for vg0912052073:

Variant ID: vg0912052073 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 12052073
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ATGATCACCTACGCATTCACCGTCCAAAAAGTGGCAATGGAGGCAACGACATGTCTCGTCACACCGGCATCGCAGATGCTGCTCCTGCAGCCGTGGTTCG[A/C]
CGGGCTGATGGCGTCCACCGCCGTCGACAGGCTCTCCTGCGTTGTGCTCTCAGCATCATCATGGAGCGGGACTTTGTCGTACGTGCGGGTGACTGAAACT

Reverse complement sequence

AGTTTCAGTCACCCGCACGTACGACAAAGTCCCGCTCCATGATGATGCTGAGAGCACAACGCAGGAGAGCCTGTCGACGGCGGTGGACGCCATCAGCCCG[T/G]
CGAACCACGGCTGCAGGAGCAGCATCTGCGATGCCGGTGTGACGAGACATGTCGTTGCCTCCATTGCCACTTTTTGGACGGTGAATGCGTAGGTGATCAT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 40.70% 23.70% 0.74% 34.83% NA
All Indica  2759 45.10% 2.70% 0.83% 51.36% NA
All Japonica  1512 33.90% 65.00% 0.40% 0.66% NA
Aus  269 17.50% 9.30% 0.74% 72.49% NA
Indica I  595 59.70% 5.70% 0.34% 34.29% NA
Indica II  465 74.60% 1.70% 0.00% 23.66% NA
Indica III  913 24.80% 0.80% 0.88% 73.60% NA
Indica Intermediate  786 40.20% 3.30% 1.65% 54.83% NA
Temperate Japonica  767 24.40% 74.80% 0.39% 0.39% NA
Tropical Japonica  504 38.90% 60.30% 0.60% 0.20% NA
Japonica Intermediate  241 53.90% 43.60% 0.00% 2.49% NA
VI/Aromatic  96 75.00% 10.40% 1.04% 13.54% NA
Intermediate  90 53.30% 31.10% 3.33% 12.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0912052073 A -> DEL N N silent_mutation Average:95.339; most accessible tissue: Zhenshan97 root, score: 97.416 N N N N
vg0912052073 A -> C LOC_Os09g20110.1 upstream_gene_variant ; 805.0bp to feature; MODIFIER silent_mutation Average:95.339; most accessible tissue: Zhenshan97 root, score: 97.416 N N N N
vg0912052073 A -> C LOC_Os09g20120.1 upstream_gene_variant ; 1755.0bp to feature; MODIFIER silent_mutation Average:95.339; most accessible tissue: Zhenshan97 root, score: 97.416 N N N N
vg0912052073 A -> C LOC_Os09g20110-LOC_Os09g20120 intergenic_region ; MODIFIER silent_mutation Average:95.339; most accessible tissue: Zhenshan97 root, score: 97.416 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)
vg0912052073 A C 0.02 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
vg0912052073 4.06E-06 NA mr1314 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
vg0912052073 NA 3.99E-06 mr1957_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