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Detailed information for vg0118445194:

Variant ID: vg0118445194 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18445194
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, T: 0.01, others allele: 0.00, population size: 90. )

Flanking Sequence (100 bp) in Reference Genome:


CGGCGATGCAGTGTGCCCATGCACCAGCGAAGGTTTTGATGGTGGTGGAGCAATGGTGTTTCTATGCTAATTGGCAGGTGGTGGACGGTGGGTGAAAACC[T/C]
AGCCCGGCCTCTGTCGGACCGACAATCGATGGTACTCAAGTGTCATTCCTCTCCTGAGGGTGTTATCGTGCCGTCTCACCCCTCAAGGGTGGTTGCTGGG

Reverse complement sequence

CCCAGCAACCACCCTTGAGGGGTGAGACGGCACGATAACACCCTCAGGAGAGGAATGACACTTGAGTACCATCGATTGTCGGTCCGACAGAGGCCGGGCT[A/G]
GGTTTTCACCCACCGTCCACCACCTGCCAATTAGCATAGAAACACCATTGCTCCACCACCATCAAAACCTTCGCTGGTGCATGGGCACACTGCATCGCCG

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 42.00% 34.10% 2.77% 21.16% NA
All Indica  2759 10.80% 50.70% 3.70% 34.87% NA
All Japonica  1512 92.30% 6.30% 1.19% 0.20% NA
Aus  269 54.30% 36.10% 2.60% 7.06% NA
Indica I  595 5.40% 49.20% 2.86% 42.52% NA
Indica II  465 20.90% 18.50% 1.94% 58.71% NA
Indica III  913 9.50% 76.30% 5.15% 8.98% NA
Indica Intermediate  786 10.30% 41.00% 3.69% 45.04% NA
Temperate Japonica  767 94.70% 3.10% 2.22% 0.00% NA
Tropical Japonica  504 88.30% 11.30% 0.00% 0.40% NA
Japonica Intermediate  241 92.90% 6.20% 0.41% 0.41% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 58.90% 18.90% 4.44% 17.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0118445194 T -> DEL N N silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33514.1 upstream_gene_variant ; 1796.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33514.2 upstream_gene_variant ; 1796.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33514.3 upstream_gene_variant ; 1796.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33500.1 downstream_gene_variant ; 3468.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33510.1 downstream_gene_variant ; 223.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33520.1 downstream_gene_variant ; 4802.0bp to feature; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 N N N N
vg0118445194 T -> C LOC_Os01g33510-LOC_Os01g33514 intergenic_region ; MODIFIER silent_mutation Average:79.76; most accessible tissue: Zhenshan97 young leaf, score: 89.559 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)
vg0118445194 T C -0.02 -0.02 -0.02 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118445194 4.03E-06 4.03E-06 mr1193 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
vg0118445194 3.84E-06 3.84E-06 mr1458 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
vg0118445194 NA 4.64E-32 mr1737 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
vg0118445194 NA 1.38E-06 mr1805 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
vg0118445194 NA 1.59E-06 mr1909 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
vg0118445194 NA 8.81E-06 mr1921 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