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Detailed information for vg1125615839:

Variant ID: vg1125615839 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 25615839
Reference Allele: TAlternative Allele: G
Primary Allele: TSecondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.96, G: 0.04, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


ATTACATTGATCTTTACCAGATACATTGGCCTGATCGGTCTGTGGAACATGGTTTCATGCCTATAACTGTGATACAGTTTCGCAGTGTTGCCATCTTGCG[T/G]
TTCTGCGCATCATTGACTTTTAATAAGGGATGTTGTGCACTTGTGCCTGCAGCTATGTCCCGATGTTTGGAGAGACAGAATATGATCCAAGCCATCAGTA

Reverse complement sequence

TACTGATGGCTTGGATCATATTCTGTCTCTCCAAACATCGGGACATAGCTGCAGGCACAAGTGCACAACATCCCTTATTAAAAGTCAATGATGCGCAGAA[A/C]
CGCAAGATGGCAACACTGCGAAACTGTATCACAGTTATAGGCATGAAACCATGTTCCACAGACCGATCAGGCCAATGTATCTGGTAAAGATCAATGTAAT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.80% 19.40% 0.36% 1.44% NA
All Indica  2759 80.90% 16.70% 0.43% 1.88% NA
All Japonica  1512 76.50% 22.60% 0.33% 0.60% NA
Aus  269 77.70% 20.80% 0.00% 1.49% NA
Indica I  595 55.30% 38.70% 0.84% 5.21% NA
Indica II  465 79.80% 19.60% 0.43% 0.22% NA
Indica III  913 95.10% 3.70% 0.00% 1.20% NA
Indica Intermediate  786 84.60% 13.60% 0.64% 1.15% NA
Temperate Japonica  767 75.40% 24.10% 0.39% 0.13% NA
Tropical Japonica  504 81.50% 17.90% 0.20% 0.40% NA
Japonica Intermediate  241 69.30% 27.80% 0.41% 2.49% NA
VI/Aromatic  96 59.40% 37.50% 0.00% 3.12% NA
Intermediate  90 78.90% 21.10% 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
vg1125615839 T -> DEL N N silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42550.1 upstream_gene_variant ; 1868.0bp to feature; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42570.1 upstream_gene_variant ; 4928.0bp to feature; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42525.1 downstream_gene_variant ; 3688.0bp to feature; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42530.1 downstream_gene_variant ; 2068.0bp to feature; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42540.1 intron_variant ; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 N N N N
vg1125615839 T -> G LOC_Os11g42540.2 intron_variant ; MODIFIER silent_mutation Average:76.286; most accessible tissue: Minghui63 flag leaf, score: 93.503 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)
vg1125615839 T G 0.0 0.01 0.01 0.0 0.0 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1125615839 NA 1.97E-06 mr1531 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
vg1125615839 3.60E-06 NA mr1644 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
vg1125615839 2.05E-08 2.24E-08 mr1644 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
vg1125615839 NA 6.59E-06 mr1989 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
vg1125615839 4.79E-07 4.36E-06 mr1191_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