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Detailed information for vg0102140552:

Variant ID: vg0102140552 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 2140552
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:


AGATTCTCACCAGCTACTTCTCAAAATCTTAAGTTTCCTCAAATAGAGGTGACGACGTTGGCTCACCACCTTTGTCGGAGACCTCTGGAGATCAGTTGCG[A/G]
ACAGGATATACGTCGAGCAACGCCATGCCACGCAACACCGCCACCTTCACTAGAGACCTATGGAGATCGAGCTCCTCGACCTTACACACCGTTAGCCTCC

Reverse complement sequence

GGAGGCTAACGGTGTGTAAGGTCGAGGAGCTCGATCTCCATAGGTCTCTAGTGAAGGTGGCGGTGTTGCGTGGCATGGCGTTGCTCGACGTATATCCTGT[T/C]
CGCAACTGATCTCCAGAGGTCTCCGACAAAGGTGGTGAGCCAACGTCGTCACCTCTATTTGAGGAAACTTAAGATTTTGAGAAGTAGCTGGTGAGAATCT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 56.90% 27.40% 0.70% 15.00% NA
All Indica  2759 74.90% 21.90% 0.25% 2.94% NA
All Japonica  1512 16.50% 42.30% 1.46% 39.81% NA
Aus  269 93.30% 0.70% 0.74% 5.20% NA
Indica I  595 31.40% 68.40% 0.17% 0.00% NA
Indica II  465 93.80% 5.20% 0.43% 0.65% NA
Indica III  913 91.20% 4.20% 0.44% 4.16% NA
Indica Intermediate  786 77.70% 17.20% 0.00% 5.09% NA
Temperate Japonica  767 22.00% 71.80% 0.52% 5.61% NA
Tropical Japonica  504 11.30% 1.40% 2.38% 84.92% NA
Japonica Intermediate  241 9.50% 33.60% 2.49% 54.36% NA
VI/Aromatic  96 69.80% 30.20% 0.00% 0.00% NA
Intermediate  90 61.10% 23.30% 2.22% 13.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0102140552 A -> G LOC_Os01g04720.1 downstream_gene_variant ; 3242.0bp to feature; MODIFIER silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 N N N N
vg0102140552 A -> G LOC_Os01g04730.1 downstream_gene_variant ; 1556.0bp to feature; MODIFIER silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 N N N N
vg0102140552 A -> G LOC_Os01g04740.1 downstream_gene_variant ; 313.0bp to feature; MODIFIER silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 N N N N
vg0102140552 A -> G LOC_Os01g04720.2 downstream_gene_variant ; 3242.0bp to feature; MODIFIER silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 N N N N
vg0102140552 A -> G LOC_Os01g04730-LOC_Os01g04740 intergenic_region ; MODIFIER silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 N N N N
vg0102140552 A -> DEL N N silent_mutation Average:77.895; most accessible tissue: Callus, score: 90.613 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)
vg0102140552 A G 0.01 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
vg0102140552 NA 8.05E-06 mr1374 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
vg0102140552 NA 5.32E-07 mr1184_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
vg0102140552 NA 7.09E-06 mr1184_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
vg0102140552 NA 5.64E-06 mr1278_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
vg0102140552 9.38E-06 9.38E-06 mr1284_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
vg0102140552 NA 9.31E-06 mr1633_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
vg0102140552 NA 1.32E-06 mr1641_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
vg0102140552 NA 1.45E-07 mr1683_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
vg0102140552 NA 4.84E-06 mr1683_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
vg0102140552 NA 9.97E-06 mr1811_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
vg0102140552 4.91E-06 4.91E-06 mr1816_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
vg0102140552 NA 9.57E-07 mr1838_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
vg0102140552 NA 3.33E-06 mr1965_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