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Detailed information for vg0828205268:

Variant ID: vg0828205268 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 28205268
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:


CGTCTTCCGGCATGATCTTGCGGGGGAGACTAAGGTGCCTATCCGCCATAATGCGCGATGCTGGAAGCACTGCGTCGCTGGCATCTTGAGCCATGATGAC[T/C]
GGCGGAGAAACGACGAGGGGCTTGGTGTGCGGAGTAGCGTGGAGTGGCGAGAATGTTAGGGCTTAGGGAGCGAGTGTGCGGGTGAGCAGTTGGCGAAAGG

Reverse complement sequence

CCTTTCGCCAACTGCTCACCCGCACACTCGCTCCCTAAGCCCTAACATTCTCGCCACTCCACGCTACTCCGCACACCAAGCCCCTCGTCGTTTCTCCGCC[A/G]
GTCATCATGGCTCAAGATGCCAGCGACGCAGTGCTTCCAGCATCGCGCATTATGGCGGATAGGCACCTTAGTCTCCCCCGCAAGATCATGCCGGAAGACG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.20% 18.40% 2.03% 0.30% NA
All Indica  2759 99.80% 0.10% 0.07% 0.00% NA
All Japonica  1512 37.20% 56.10% 5.82% 0.93% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 18.90% 75.10% 6.00% 0.00% NA
Tropical Japonica  504 56.30% 37.30% 3.57% 2.78% NA
Japonica Intermediate  241 55.20% 34.90% 9.96% 0.00% NA
VI/Aromatic  96 95.80% 3.10% 1.04% 0.00% NA
Intermediate  90 76.70% 17.80% 5.56% 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
vg0828205268 T -> C LOC_Os08g44910.1 upstream_gene_variant ; 2547.0bp to feature; MODIFIER silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 N N N N
vg0828205268 T -> C LOC_Os08g44920.1 upstream_gene_variant ; 7.0bp to feature; MODIFIER silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 N N N N
vg0828205268 T -> C LOC_Os08g44930.1 downstream_gene_variant ; 3482.0bp to feature; MODIFIER silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 N N N N
vg0828205268 T -> C LOC_Os08g44930.2 downstream_gene_variant ; 3482.0bp to feature; MODIFIER silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 N N N N
vg0828205268 T -> C LOC_Os08g44920-LOC_Os08g44930 intergenic_region ; MODIFIER silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 N N N N
vg0828205268 T -> DEL N N silent_mutation Average:76.514; most accessible tissue: Minghui63 flag leaf, score: 94.293 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)
vg0828205268 T C 0.0 0.01 0.01 0.01 0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0828205268 NA 8.52E-06 mr1153_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
vg0828205268 NA 1.79E-08 mr1659_2 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