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Detailed information for vg0125159819:

Variant ID: vg0125159819 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 25159819
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.87, A: 0.13, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


TGCGGCTGGCGGCGCCGCGCAGCCTCGCCCTCGGCGTCACAGTGCACCACGCCGCATGCGACAGCGTGAGCACGACACACTCCACACCTGCGCTGCCTCT[A/G]
CTCCGCCGCCGGTTGGATCCTCACCGTCTGGGTGGCTGGGACACCCGGAGGTGGAGAAGAAGGAGAGGAGAGGGGCTGACGGGTGGGGTCCACGTTTGTT

Reverse complement sequence

AACAAACGTGGACCCCACCCGTCAGCCCCTCTCCTCTCCTTCTTCTCCACCTCCGGGTGTCCCAGCCACCCAGACGGTGAGGATCCAACCGGCGGCGGAG[T/C]
AGAGGCAGCGCAGGTGTGGAGTGTGTCGTGCTCACGCTGTCGCATGCGGCGTGGTGCACTGTGACGCCGAGGGCGAGGCTGCGCGGCGCCGCCAGCCGCA

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 69.10% 30.70% 0.15% 0.00% NA
All Indica  2759 98.20% 1.60% 0.18% 0.00% NA
All Japonica  1512 15.30% 84.70% 0.00% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.50% 0.34% 0.00% NA
Indica II  465 99.10% 0.60% 0.22% 0.00% NA
Indica III  913 96.70% 3.30% 0.00% 0.00% NA
Indica Intermediate  786 98.60% 1.10% 0.25% 0.00% NA
Temperate Japonica  767 1.00% 99.00% 0.00% 0.00% NA
Tropical Japonica  504 36.10% 63.90% 0.00% 0.00% NA
Japonica Intermediate  241 17.00% 83.00% 0.00% 0.00% NA
VI/Aromatic  96 9.40% 90.60% 0.00% 0.00% NA
Intermediate  90 55.60% 42.20% 2.22% 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
vg0125159819 A -> G LOC_Os01g43910.1 upstream_gene_variant ; 1440.0bp to feature; MODIFIER silent_mutation Average:88.099; most accessible tissue: Zhenshan97 flag leaf, score: 92.686 N N N N
vg0125159819 A -> G LOC_Os01g43910-LOC_Os01g43920 intergenic_region ; MODIFIER silent_mutation Average:88.099; most accessible tissue: Zhenshan97 flag leaf, score: 92.686 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)
vg0125159819 A G -0.01 -0.01 -0.01 0.0 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0125159819 NA 2.19E-66 mr1027 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
vg0125159819 NA 2.06E-17 mr1133 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
vg0125159819 NA 3.41E-12 mr1188 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
vg0125159819 NA 2.24E-07 mr1188 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
vg0125159819 NA 2.60E-21 mr1217 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
vg0125159819 NA 1.24E-06 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
vg0125159819 NA 1.29E-28 mr1414 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
vg0125159819 NA 5.44E-20 mr1845 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
vg0125159819 8.48E-07 NA mr1949 Jap_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
vg0125159819 NA 5.93E-07 mr1188_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
vg0125159819 NA 1.37E-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
vg0125159819 NA 3.07E-34 mr1448_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
vg0125159819 NA 5.16E-32 mr1841_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