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Detailed information for vg0818820911:

Variant ID: vg0818820911 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 18820911
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATCTTGTTCGTATTGGTTTATTACACCAGATTAAATCACTCTGCTCGTATCAACCACTGAAGTAGAACTTCGTACTGTGCTATCTGTTCTCATATCACT[A/G]
CTGATCTTTGCTGGGTGGTGCAAATAGTCCCGGTTCGAATAGAAAAATAGACTAAACATCATTTTTAGCTCTGGTTAAAAAGCCAACGAAACTTTTTGAT

Reverse complement sequence

ATCAAAAAGTTTCGTTGGCTTTTTAACCAGAGCTAAAAATGATGTTTAGTCTATTTTTCTATTCGAACCGGGACTATTTGCACCACCCAGCAAAGATCAG[T/C]
AGTGATATGAGAACAGATAGCACAGTACGAAGTTCTACTTCAGTGGTTGATACGAGCAGAGTGATTTAATCTGGTGTAATAAACCAATACGAACAAGATT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 81.60% 3.00% 0.49% 14.92% NA
All Indica  2759 78.80% 1.10% 0.58% 19.61% NA
All Japonica  1512 89.00% 0.00% 0.46% 10.52% NA
Aus  269 58.40% 41.60% 0.00% 0.00% NA
Indica I  595 95.30% 0.00% 0.50% 4.20% NA
Indica II  465 90.50% 2.40% 0.43% 6.67% NA
Indica III  913 69.00% 0.20% 0.66% 30.12% NA
Indica Intermediate  786 70.60% 2.00% 0.64% 26.72% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 69.80% 0.00% 1.19% 28.97% NA
Japonica Intermediate  241 94.20% 0.00% 0.41% 5.39% NA
VI/Aromatic  96 99.00% 0.00% 0.00% 1.04% NA
Intermediate  90 94.40% 1.10% 0.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0818820911 A -> G LOC_Os08g30554.1 upstream_gene_variant ; 354.0bp to feature; MODIFIER silent_mutation Average:64.369; most accessible tissue: Zhenshan97 panicle, score: 94.811 N N N N
vg0818820911 A -> G LOC_Os08g30560.1 downstream_gene_variant ; 4505.0bp to feature; MODIFIER silent_mutation Average:64.369; most accessible tissue: Zhenshan97 panicle, score: 94.811 N N N N
vg0818820911 A -> G LOC_Os08g30550-LOC_Os08g30554 intergenic_region ; MODIFIER silent_mutation Average:64.369; most accessible tissue: Zhenshan97 panicle, score: 94.811 N N N N
vg0818820911 A -> DEL N N silent_mutation Average:64.369; most accessible tissue: Zhenshan97 panicle, score: 94.811 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)
vg0818820911 A G 0.05 0.0 0.01 0.05 0.04 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0818820911 NA 1.53E-06 mr1073 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
vg0818820911 NA 7.25E-06 mr1387 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
vg0818820911 NA 4.25E-06 mr1398 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
vg0818820911 3.44E-06 3.44E-06 mr1694 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
vg0818820911 5.82E-06 5.86E-07 mr1761 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
vg0818820911 NA 2.97E-06 mr1857 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
vg0818820911 NA 3.67E-07 mr1928 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
vg0818820911 NA 1.01E-06 mr1263_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
vg0818820911 NA 2.21E-06 mr1294_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
vg0818820911 NA 4.49E-06 mr1638_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
vg0818820911 NA 5.87E-06 mr1813_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