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Detailed information for vg0111174891:

Variant ID: vg0111174891 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 11174891
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AAATTAAATTATTTTTATTGCTTTATTTATTTTTCTAAGGTTATCAGCCATAGCTACCCAGGTAGCTTTGTGTCCGGAAGTCTTATGGTGTGAAATGGGG[T/C]
GTCTATTATTTAGATCTTTCTCGAGGTGAGTATAGCTCATTGACTGATTGACATGATCAAGATATTTTTCCACATCATCGTAGTATCTTATTAATATATT

Reverse complement sequence

AATATATTAATAAGATACTACGATGATGTGGAAAAATATCTTGATCATGTCAATCAGTCAATGAGCTATACTCACCTCGAGAAAGATCTAAATAATAGAC[A/G]
CCCCATTTCACACCATAAGACTTCCGGACACAAAGCTACCTGGGTAGCTATGGCTGATAACCTTAGAAAAATAAATAAAGCAATAAAAATAATTTAATTT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.20% 5.80% 2.01% 0.00% NA
All Indica  2759 87.00% 9.80% 3.23% 0.00% NA
All Japonica  1512 99.90% 0.00% 0.13% 0.00% NA
Aus  269 98.50% 0.00% 1.49% 0.00% NA
Indica I  595 83.00% 9.70% 7.23% 0.00% NA
Indica II  465 95.50% 2.60% 1.94% 0.00% NA
Indica III  913 87.30% 12.20% 0.55% 0.00% NA
Indica Intermediate  786 84.60% 11.30% 4.07% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.20% 0.00% NA
Japonica Intermediate  241 99.60% 0.00% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg0111174891 T -> C LOC_Os01g19694.1 downstream_gene_variant ; 439.0bp to feature; MODIFIER silent_mutation Average:73.929; most accessible tissue: Zhenshan97 root, score: 93.592 N N N N
vg0111174891 T -> C LOC_Os01g19710.1 downstream_gene_variant ; 2233.0bp to feature; MODIFIER silent_mutation Average:73.929; most accessible tissue: Zhenshan97 root, score: 93.592 N N N N
vg0111174891 T -> C LOC_Os01g19694-LOC_Os01g19710 intergenic_region ; MODIFIER silent_mutation Average:73.929; most accessible tissue: Zhenshan97 root, score: 93.592 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)
vg0111174891 T C -0.11 -0.06 -0.04 -0.04 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0111174891 NA 7.97E-11 mr1968_2 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