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Detailed information for vg0506784564:

Variant ID: vg0506784564 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 6784564
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTTGACCCCTGCATTGCACAGACAGGCTAGCTCTCAACGCTGGCGGCTCGCACCTCACCTCTTCACACATTAGCTTTTCCCAAATCCAAGCTGTTCTA[G/A]
GCTAGCTAGCTCTGGCTACTTCTTCTCTTCCCATGAAATTATTAACGACTTTGACACATGCATGTGCGTACTATATACCTCTAATTAAACAATTCATAAC

Reverse complement sequence

GTTATGAATTGTTTAATTAGAGGTATATAGTACGCACATGCATGTGTCAAAGTCGTTAATAATTTCATGGGAAGAGAAGAAGTAGCCAGAGCTAGCTAGC[C/T]
TAGAACAGCTTGGATTTGGGAAAAGCTAATGTGTGAAGAGGTGAGGTGCGAGCCGCCAGCGTTGAGAGCTAGCCTGTCTGTGCAATGCAGGGGTCAAACC

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 62.90% 37.10% 0.02% 0.00% NA
All Indica  2759 95.50% 4.50% 0.00% 0.00% NA
All Japonica  1512 4.80% 95.20% 0.00% 0.00% NA
Aus  269 82.20% 17.80% 0.00% 0.00% NA
Indica I  595 98.80% 1.20% 0.00% 0.00% NA
Indica II  465 95.90% 4.10% 0.00% 0.00% NA
Indica III  913 93.20% 6.80% 0.00% 0.00% NA
Indica Intermediate  786 95.50% 4.50% 0.00% 0.00% NA
Temperate Japonica  767 1.70% 98.30% 0.00% 0.00% NA
Tropical Japonica  504 5.20% 94.80% 0.00% 0.00% NA
Japonica Intermediate  241 13.70% 86.30% 0.00% 0.00% NA
VI/Aromatic  96 1.00% 99.00% 0.00% 0.00% NA
Intermediate  90 46.70% 52.20% 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
vg0506784564 G -> A LOC_Os05g11910.1 upstream_gene_variant ; 3112.0bp to feature; MODIFIER silent_mutation Average:77.467; most accessible tissue: Callus, score: 99.347 N N N N
vg0506784564 G -> A LOC_Os05g11900-LOC_Os05g11910 intergenic_region ; MODIFIER silent_mutation Average:77.467; most accessible tissue: Callus, score: 99.347 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)
vg0506784564 G A 0.11 -0.05 -0.03 -0.12 -0.13 -0.07

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0506784564 NA 1.34E-25 mr1039 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
vg0506784564 NA 7.93E-27 mr1632 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
vg0506784564 NA 5.66E-42 mr1873 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
vg0506784564 7.62E-06 NA mr1071_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
vg0506784564 NA 1.52E-27 mr1238_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
vg0506784564 6.70E-09 NA mr1613_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
vg0506784564 NA 3.09E-34 mr1632_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
vg0506784564 NA 1.21E-32 mr1873_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