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Detailed information for vg0208784668:

Variant ID: vg0208784668 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8784668
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAGTTTCAACTTTCAGTTCAGAAAGGGCTTTGTGTTCAACATGCGCGGTCGCCCACTCCCACGGTCATCTACATCTAAGCATGTGGATCTCCCTCCACTC[G/A]
TTTTCTGCGTGCATAATTCCCAAACTGCCGATGTGTTCTTTAAAAAAAGTTTCTATACGAAAGTTACTTAAAAAAATCATATTGTTCTATTTTTTTAAAA

Reverse complement sequence

TTTTAAAAAAATAGAACAATATGATTTTTTTAAGTAACTTTCGTATAGAAACTTTTTTTAAAGAACACATCGGCAGTTTGGGAATTATGCACGCAGAAAA[C/T]
GAGTGGAGGGAGATCCACATGCTTAGATGTAGATGACCGTGGGAGTGGGCGACCGCGCATGTTGAACACAAAGCCCTTTCTGAACTGAAAGTTGAAACTT

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 84.50% 15.50% 0.02% 0.00% NA
All Indica  2759 82.00% 18.00% 0.00% 0.00% NA
All Japonica  1512 99.20% 0.80% 0.00% 0.00% NA
Aus  269 25.30% 74.30% 0.37% 0.00% NA
Indica I  595 71.80% 28.20% 0.00% 0.00% NA
Indica II  465 66.70% 33.30% 0.00% 0.00% NA
Indica III  913 94.10% 5.90% 0.00% 0.00% NA
Indica Intermediate  786 84.70% 15.30% 0.00% 0.00% NA
Temperate Japonica  767 99.20% 0.80% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 88.50% 11.50% 0.00% 0.00% NA
Intermediate  90 87.80% 12.20% 0.00% 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
vg0208784668 G -> A LOC_Os02g15620.1 downstream_gene_variant ; 3045.0bp to feature; MODIFIER silent_mutation Average:89.083; most accessible tissue: Minghui63 root, score: 97.42 N N N N
vg0208784668 G -> A LOC_Os02g15630.1 intron_variant ; MODIFIER silent_mutation Average:89.083; most accessible tissue: Minghui63 root, score: 97.42 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)
vg0208784668 G A -0.04 -0.02 -0.01 0.01 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208784668 NA 4.20E-06 mr1185 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
vg0208784668 NA 7.71E-08 mr1392 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
vg0208784668 NA 2.08E-07 mr1420 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
vg0208784668 NA 5.08E-07 mr1507 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
vg0208784668 NA 6.82E-07 mr1556 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
vg0208784668 NA 2.21E-07 mr1764 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
vg0208784668 NA 1.93E-08 mr1884 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
vg0208784668 NA 6.46E-06 mr1952 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