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Detailed information for vg0501337655:

Variant ID: vg0501337655 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 1337655
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:


TTTTGGTGGTCACATTGCATGGTGCCCTTAGCAATTTGTTTTCGAACACTGTTTGACTAACAGATGAGACAACGCCTTCAAAGAATGCCCACTTGGATAT[A/T]
TATCAATATATGCATGCATGAACGTACGACGATCTCTTTCCTAACTACGTGCCAGCATGCAATGCATGCATGCCGTTAATTTAGCTGTGTCCCTAGCTAG

Reverse complement sequence

CTAGCTAGGGACACAGCTAAATTAACGGCATGCATGCATTGCATGCTGGCACGTAGTTAGGAAAGAGATCGTCGTACGTTCATGCATGCATATATTGATA[T/A]
ATATCCAAGTGGGCATTCTTTGAAGGCGTTGTCTCATCTGTTAGTCAAACAGTGTTCGAAAACAAATTGCTAAGGGCACCATGCAATGTGACCACCAAAA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 88.20% 0.90% 3.53% 7.38% NA
All Indica  2759 83.80% 0.70% 3.62% 11.89% NA
All Japonica  1512 93.20% 1.30% 4.23% 1.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 94.80% 0.00% 1.18% 4.03% NA
Indica II  465 89.00% 1.10% 3.23% 6.67% NA
Indica III  913 72.50% 0.80% 6.57% 20.15% NA
Indica Intermediate  786 85.50% 0.90% 2.29% 11.32% NA
Temperate Japonica  767 97.30% 0.40% 0.39% 1.96% NA
Tropical Japonica  504 86.30% 2.80% 10.32% 0.60% NA
Japonica Intermediate  241 94.60% 1.20% 3.73% 0.41% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 3.30% 3.33% 2.22% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0501337655 A -> T LOC_Os05g03290.1 upstream_gene_variant ; 1363.0bp to feature; MODIFIER silent_mutation Average:61.547; most accessible tissue: Minghui63 root, score: 94.021 N N N N
vg0501337655 A -> T LOC_Os05g03299.1 downstream_gene_variant ; 3040.0bp to feature; MODIFIER silent_mutation Average:61.547; most accessible tissue: Minghui63 root, score: 94.021 N N N N
vg0501337655 A -> T LOC_Os05g03290-LOC_Os05g03299 intergenic_region ; MODIFIER silent_mutation Average:61.547; most accessible tissue: Minghui63 root, score: 94.021 N N N N
vg0501337655 A -> DEL N N silent_mutation Average:61.547; most accessible tissue: Minghui63 root, score: 94.021 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)
vg0501337655 A T 0.01 0.02 -0.01 -0.03 0.02 0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0501337655 NA 7.04E-06 mr1006 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
vg0501337655 NA 9.49E-07 mr1662 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
vg0501337655 NA 1.73E-08 mr1870 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
vg0501337655 NA 4.20E-06 mr1679_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
vg0501337655 NA 1.94E-06 mr1870_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