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Detailed information for vg0109557806:

Variant ID: vg0109557806 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 9557806
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


ACACGTGTGTGTGTCTGTATTACATGTGCCACGAATCATGTGCACACGGTCACACACAGATATCGATCAGAACGAACGAGAGAAGGGAAAGCGATCGTGC[G/T]
ATGATAAAAATCACTGCAAGATCAGATCAGTTTTGATATGTGGAAGTTGATGTAAAATAAAGCTGTTTTGGTTTGTGGTACACCACGCACACTGCATCAG

Reverse complement sequence

CTGATGCAGTGTGCGTGGTGTACCACAAACCAAAACAGCTTTATTTTACATCAACTTCCACATATCAAAACTGATCTGATCTTGCAGTGATTTTTATCAT[C/A]
GCACGATCGCTTTCCCTTCTCTCGTTCGTTCTGATCGATATCTGTGTGTGACCGTGTGCACATGATTCGTGGCACATGTAATACAGACACACACACGTGT

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 93.20% 3.60% 3.20% 0.00% NA
All Indica  2759 89.60% 5.40% 5.00% 0.00% NA
All Japonica  1512 97.90% 1.50% 0.60% 0.00% NA
Aus  269 99.60% 0.00% 0.37% 0.00% NA
Indica I  595 83.50% 6.60% 9.92% 0.00% NA
Indica II  465 90.10% 5.60% 4.30% 0.00% NA
Indica III  913 97.90% 1.80% 0.33% 0.00% NA
Indica Intermediate  786 84.40% 8.50% 7.12% 0.00% NA
Temperate Japonica  767 99.30% 0.50% 0.13% 0.00% NA
Tropical Japonica  504 95.60% 3.20% 1.19% 0.00% NA
Japonica Intermediate  241 98.30% 0.80% 0.83% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 95.60% 2.20% 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
vg0109557806 G -> T LOC_Os01g16800-LOC_Os01g16810 intergenic_region ; MODIFIER silent_mutation Average:79.746; most accessible tissue: Zhenshan97 panicle, score: 97.661 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)
vg0109557806 G T -0.07 -0.06 -0.07 -0.02 -0.08 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0109557806 NA 1.30E-06 mr1236 Ind_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
vg0109557806 NA 9.10E-06 mr1327 Ind_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
vg0109557806 NA 2.37E-06 mr1629 Ind_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
vg0109557806 NA 2.84E-06 mr1629_2 Ind_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