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Detailed information for vg0817661366:

Variant ID: vg0817661366 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 17661366
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCGGAGACGGCGCCCTCCCAACGGCGGCGTCGACAGCGTCCGCGCTCCCTCTCCCGCTCTCCTTCCTGTCTCGCTGGCACGGTGTAGCGACGACGGGTGC[G/A]
GCGGATTTTTTTTTGCAATTTTTTCCATGGCTATTGCTAACCAAATCGGATTGTGTACGGACGAAAATTAGATGTGACGAAAGAAAAAATACGAATATTT

Reverse complement sequence

AAATATTCGTATTTTTTCTTTCGTCACATCTAATTTTCGTCCGTACACAATCCGATTTGGTTAGCAATAGCCATGGAAAAAATTGCAAAAAAAAATCCGC[C/T]
GCACCCGTCGTCGCTACACCGTGCCAGCGAGACAGGAAGGAGAGCGGGAGAGGGAGCGCGGACGCTGTCGACGCCGCCGTTGGGAGGGCGCCGTCTCCGC

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 85.80% 10.60% 2.14% 1.54% NA
All Indica  2759 96.20% 1.60% 1.30% 0.91% NA
All Japonica  1512 71.90% 28.10% 0.00% 0.00% NA
Aus  269 56.50% 4.50% 21.56% 17.47% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 98.70% 0.40% 0.22% 0.65% NA
Indica III  913 95.20% 2.20% 1.75% 0.88% NA
Indica Intermediate  786 93.00% 2.90% 2.29% 1.78% NA
Temperate Japonica  767 98.00% 2.00% 0.00% 0.00% NA
Tropical Japonica  504 31.20% 68.80% 0.00% 0.00% NA
Japonica Intermediate  241 73.90% 26.10% 0.00% 0.00% NA
VI/Aromatic  96 90.60% 8.30% 1.04% 0.00% NA
Intermediate  90 82.20% 10.00% 6.67% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0817661366 G -> A LOC_Os08g28880.1 upstream_gene_variant ; 2214.0bp to feature; MODIFIER silent_mutation Average:89.733; most accessible tissue: Minghui63 panicle, score: 97.008 N N N N
vg0817661366 G -> A LOC_Os08g28870-LOC_Os08g28880 intergenic_region ; MODIFIER silent_mutation Average:89.733; most accessible tissue: Minghui63 panicle, score: 97.008 N N N N
vg0817661366 G -> DEL N N silent_mutation Average:89.733; most accessible tissue: Minghui63 panicle, score: 97.008 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)
vg0817661366 G A 0.0 -0.01 -0.01 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0817661366 NA 1.21E-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
vg0817661366 3.24E-06 NA mr1261 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
vg0817661366 NA 9.15E-11 mr1578 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
vg0817661366 NA 1.96E-06 mr1627 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
vg0817661366 NA 4.05E-18 mr1715 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
vg0817661366 NA 1.99E-18 mr1301_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
vg0817661366 NA 1.69E-06 mr1524_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
vg0817661366 NA 1.26E-17 mr1578_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
vg0817661366 NA 7.75E-10 mr1819_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
vg0817661366 NA 3.72E-11 mr1851_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
vg0817661366 NA 8.69E-07 mr1860_2 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
vg0817661366 NA 1.07E-15 mr1864_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
vg0817661366 NA 3.32E-09 mr1952_2 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