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Detailed information for vg0826027845:

Variant ID: vg0826027845 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 26027845
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTAGTACAACATTACAACAGTGCTCTCTCGTTTTAGAGCCTGTTTAGTTACCAAACAAAATTTTTCACGTTGTCACATAGAATGTTTAGACACATGCATA[G/A]
AGTATTAAATGTAGAAAAAAAAACAATTATACAGTTTGCCAGGAAATTGCGAGACAAATCTTTTAAGCCTAATTGCGGCATGATTTGACAATGTAGTTAT

Reverse complement sequence

ATAACTACATTGTCAAATCATGCCGCAATTAGGCTTAAAAGATTTGTCTCGCAATTTCCTGGCAAACTGTATAATTGTTTTTTTTTCTACATTTAATACT[C/T]
TATGCATGTGTCTAAACATTCTATGTGACAACGTGAAAAATTTTGTTTGGTAACTAAACAGGCTCTAAAACGAGAGAGCACTGTTGTAATGTTGTACTAC

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 64.30% 35.50% 0.15% 0.00% NA
All Indica  2759 98.70% 1.20% 0.11% 0.00% NA
All Japonica  1512 3.00% 97.00% 0.00% 0.00% NA
Aus  269 77.30% 21.60% 1.12% 0.00% NA
Indica I  595 99.20% 0.70% 0.17% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 99.50% 0.40% 0.11% 0.00% NA
Indica Intermediate  786 97.80% 2.20% 0.00% 0.00% NA
Temperate Japonica  767 2.60% 97.40% 0.00% 0.00% NA
Tropical Japonica  504 2.00% 98.00% 0.00% 0.00% NA
Japonica Intermediate  241 6.20% 93.80% 0.00% 0.00% NA
VI/Aromatic  96 20.80% 79.20% 0.00% 0.00% NA
Intermediate  90 48.90% 50.00% 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
vg0826027845 G -> A LOC_Os08g41200.1 upstream_gene_variant ; 4255.0bp to feature; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 N N N N
vg0826027845 G -> A LOC_Os08g41220.1 downstream_gene_variant ; 324.0bp to feature; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 N N N N
vg0826027845 G -> A LOC_Os08g41210.4 downstream_gene_variant ; 1667.0bp to feature; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 N N N N
vg0826027845 G -> A LOC_Os08g41210.3 downstream_gene_variant ; 622.0bp to feature; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 N N N N
vg0826027845 G -> A LOC_Os08g41210.1 intron_variant ; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 N N N N
vg0826027845 G -> A LOC_Os08g41210.2 intron_variant ; MODIFIER silent_mutation Average:82.003; most accessible tissue: Minghui63 root, score: 94.652 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)
vg0826027845 G A 0.02 0.05 0.04 0.01 0.04 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0826027845 NA 4.71E-22 mr1021 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
vg0826027845 NA 6.55E-15 mr1228 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
vg0826027845 NA 2.08E-16 mr1323 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
vg0826027845 NA 1.30E-10 mr1325 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
vg0826027845 NA 1.50E-12 mr1326 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
vg0826027845 NA 1.97E-21 mr1477 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
vg0826027845 NA 1.59E-08 mr1299_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
vg0826027845 NA 2.72E-41 mr1689_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
vg0826027845 NA 2.80E-08 mr1700_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
vg0826027845 NA 8.81E-07 mr1727_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