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Detailed information for vg0101944598:

Variant ID: vg0101944598 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 1944598
Reference Allele: TAlternative Allele: G
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.06, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


ACCTCGGGCTTCTTGACCTCAGCCTTGGGCACGGTGACGGTGAGCACGCCGTTCTCCATGCTGGCCTTCACCTGGTCCACCTTGGCGTTCTCCGGCAGCC[T/G]
GAACCGCCGCATGAACTGCCCGCTGCTGCGCTCCACGCGGTGCCACTTGTCGTTCTTGTCCTCCTTCTCCTTGCTGCGCTGCCCGCTGATCACCAGCACG

Reverse complement sequence

CGTGCTGGTGATCAGCGGGCAGCGCAGCAAGGAGAAGGAGGACAAGAACGACAAGTGGCACCGCGTGGAGCGCAGCAGCGGGCAGTTCATGCGGCGGTTC[A/C]
GGCTGCCGGAGAACGCCAAGGTGGACCAGGTGAAGGCCAGCATGGAGAACGGCGTGCTCACCGTCACCGTGCCCAAGGCTGAGGTCAAGAAGCCCGAGGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.70% 41.00% 0.04% 0.23% NA
All Indica  2759 85.00% 14.60% 0.04% 0.40% NA
All Japonica  1512 24.10% 75.80% 0.07% 0.00% NA
Aus  269 4.10% 95.90% 0.00% 0.00% NA
Indica I  595 97.30% 2.50% 0.00% 0.17% NA
Indica II  465 94.20% 5.60% 0.00% 0.22% NA
Indica III  913 76.10% 23.40% 0.11% 0.33% NA
Indica Intermediate  786 80.50% 18.70% 0.00% 0.76% NA
Temperate Japonica  767 15.60% 84.20% 0.13% 0.00% NA
Tropical Japonica  504 45.00% 55.00% 0.00% 0.00% NA
Japonica Intermediate  241 7.50% 92.50% 0.00% 0.00% NA
VI/Aromatic  96 4.20% 95.80% 0.00% 0.00% NA
Intermediate  90 55.60% 44.40% 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
vg0101944598 T -> G LOC_Os01g04360.1 synonymous_variant ; p.Arg109Arg; LOW synonymous_codon Average:85.782; most accessible tissue: Minghui63 panicle, score: 97.431 N N N N
vg0101944598 T -> DEL LOC_Os01g04360.1 N frameshift_variant Average:85.782; most accessible tissue: Minghui63 panicle, score: 97.431 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)
vg0101944598 T G 0.0 -0.01 -0.02 -0.01 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0101944598 NA 1.31E-06 Yield Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg0101944598 NA 1.19E-08 mr1465 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
vg0101944598 NA 1.70E-06 mr1925 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
vg0101944598 NA 3.00E-10 mr1228_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
vg0101944598 NA 2.38E-23 mr1401_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