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Detailed information for vg0109548538:

Variant ID: vg0109548538 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9548538
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGTAACAAAAAAAACAAAAAATCTGACCGTTTTAAGGTTACAATTTTGTCAGAATTTTATCTTTTTTGTTATTCTCTATGTAGAATGAATTTGAATAT[G/T]
CGACTTTGCACGTAGATGTAATACTATTAAAAGTACATGTATGAATTTTCCTAGAATTTTTTGTGAAAATTTTTAGTTGGTGTACACGGTGTGTACACGC

Reverse complement sequence

GCGTGTACACACCGTGTACACCAACTAAAAATTTTCACAAAAAATTCTAGGAAAATTCATACATGTACTTTTAATAGTATTACATCTACGTGCAAAGTCG[C/A]
ATATTCAAATTCATTCTACATAGAGAATAACAAAAAAGATAAAATTCTGACAAAATTGTAACCTTAAAACGGTCAGATTTTTTGTTTTTTTTGTTACGGC

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 48.50% 0.10% 14.96% 36.44% NA
All Indica  2759 58.20% 0.00% 21.24% 20.48% NA
All Japonica  1512 23.30% 0.00% 5.29% 71.43% NA
Aus  269 91.80% 1.10% 3.72% 3.35% NA
Indica I  595 48.10% 0.20% 35.46% 16.30% NA
Indica II  465 54.80% 0.00% 19.78% 25.38% NA
Indica III  913 64.30% 0.00% 13.58% 22.12% NA
Indica Intermediate  786 60.90% 0.00% 20.23% 18.83% NA
Temperate Japonica  767 11.70% 0.00% 6.13% 82.14% NA
Tropical Japonica  504 37.50% 0.00% 3.37% 59.13% NA
Japonica Intermediate  241 30.30% 0.00% 6.64% 63.07% NA
VI/Aromatic  96 43.80% 0.00% 17.71% 38.54% NA
Intermediate  90 50.00% 0.00% 15.56% 34.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0109548538 G -> T LOC_Os01g16800.1 upstream_gene_variant ; 2499.0bp to feature; MODIFIER silent_mutation Average:69.85; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 N N N N
vg0109548538 G -> T LOC_Os01g16800-LOC_Os01g16810 intergenic_region ; MODIFIER silent_mutation Average:69.85; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 N N N N
vg0109548538 G -> DEL N N silent_mutation Average:69.85; most accessible tissue: Zhenshan97 flag leaf, score: 87.282 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)
vg0109548538 G T 0.01 0.0 -0.01 -0.02 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109548538 NA 7.67E-38 mr1486 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
vg0109548538 NA 4.20E-07 mr1577 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
vg0109548538 4.39E-06 4.39E-06 mr1577 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
vg0109548538 3.38E-07 3.08E-21 mr1679 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
vg0109548538 NA 7.63E-06 mr1686 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
vg0109548538 NA 9.07E-07 mr1704 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
vg0109548538 NA 8.73E-13 mr1741 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
vg0109548538 NA 2.78E-17 mr1768 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
vg0109548538 NA 6.65E-08 mr1815 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
vg0109548538 2.52E-07 2.52E-07 mr1815 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
vg0109548538 1.61E-06 8.50E-15 mr1879 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
vg0109548538 NA 6.42E-21 mr1679_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
vg0109548538 NA 1.17E-08 mr1741_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
vg0109548538 NA 9.18E-17 mr1746_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