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Detailed information for vg0916047184:

Variant ID: vg0916047184 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 16047184
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.53, G: 0.47, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:


TCGGGGTGGCCGATACAGAGCCGACGAAGCCGTATTCGGTCAGACTGAGCCGATGGCGGTCTGACCGAGCCAAGGCCGGTCTGACCGCCCGCTCAACGCC[A/G]
GTCTGATCGGCCATGCCGATGGGGCCCTCTGACAGCACTACAACGGCTAGTTTTCTAGCCGTTGCAGAGTAGCACGGTCCGACCGGCCACATACCTCCGG

Reverse complement sequence

CCGGAGGTATGTGGCCGGTCGGACCGTGCTACTCTGCAACGGCTAGAAAACTAGCCGTTGTAGTGCTGTCAGAGGGCCCCATCGGCATGGCCGATCAGAC[T/C]
GGCGTTGAGCGGGCGGTCAGACCGGCCTTGGCTCGGTCAGACCGCCATCGGCTCAGTCTGACCGAATACGGCTTCGTCGGCTCTGTATCGGCCACCCCGA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 37.70% 9.50% 0.23% 52.60% NA
All Indica  2759 4.50% 13.60% 0.40% 81.44% NA
All Japonica  1512 99.10% 0.20% 0.00% 0.73% NA
Aus  269 2.60% 23.40% 0.00% 73.98% NA
Indica I  595 4.20% 35.80% 0.34% 59.66% NA
Indica II  465 3.70% 8.40% 0.22% 87.74% NA
Indica III  913 2.50% 2.60% 0.55% 94.30% NA
Indica Intermediate  786 7.60% 12.70% 0.38% 79.26% NA
Temperate Japonica  767 99.50% 0.10% 0.00% 0.39% NA
Tropical Japonica  504 98.20% 0.40% 0.00% 1.39% NA
Japonica Intermediate  241 99.60% 0.00% 0.00% 0.41% NA
VI/Aromatic  96 96.90% 1.00% 0.00% 2.08% NA
Intermediate  90 63.30% 6.70% 0.00% 30.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0916047184 A -> G LOC_Os09g26540.1 upstream_gene_variant ; 1717.0bp to feature; MODIFIER silent_mutation Average:37.58; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0916047184 A -> G LOC_Os09g26550.2 upstream_gene_variant ; 1954.0bp to feature; MODIFIER silent_mutation Average:37.58; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0916047184 A -> G LOC_Os09g26540.2 upstream_gene_variant ; 1717.0bp to feature; MODIFIER silent_mutation Average:37.58; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0916047184 A -> G LOC_Os09g26540-LOC_Os09g26550 intergenic_region ; MODIFIER silent_mutation Average:37.58; most accessible tissue: Minghui63 young leaf, score: 83.419 N N N N
vg0916047184 A -> DEL N N silent_mutation Average:37.58; most accessible tissue: Minghui63 young leaf, score: 83.419 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)
vg0916047184 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
vg0916047184 NA 3.76E-09 mr1707 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
vg0916047184 NA 1.34E-07 mr1707 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
vg0916047184 NA 1.88E-12 mr1728 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
vg0916047184 NA 4.69E-09 mr1728 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
vg0916047184 NA 5.99E-07 mr1860 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
vg0916047184 NA 2.44E-07 mr1020_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
vg0916047184 NA 2.95E-08 mr1355_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
vg0916047184 NA 3.92E-06 mr1452_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
vg0916047184 NA 3.12E-06 mr1707_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
vg0916047184 NA 8.22E-15 mr1728_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
vg0916047184 NA 2.03E-09 mr1728_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
vg0916047184 NA 7.62E-07 mr1860_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
vg0916047184 NA 2.30E-08 mr1895_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
vg0916047184 NA 6.55E-08 mr1899_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
vg0916047184 NA 1.48E-06 mr1899_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
vg0916047184 NA 1.55E-07 mr1910_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
vg0916047184 NA 3.31E-06 mr1928_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
vg0916047184 NA 9.68E-07 mr1928_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