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Detailed information for vg0118657999:

Variant ID: vg0118657999 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 18657999
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.62, G: 0.38, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:


ACCGATAGTGTTGACTTAGTCTTCATTTTACGTGGCGTTTATGTGACATTAAAATTAAAAGAATATGTGTGACCCATTTATCCGTCAAAAAGAATATTAT[A/G]
GGGCCACGTATCATCCTCTCTTTTAACACTTCTTCCTCCTTCCTCTCATCTCTCCCTTATCTCTCTTTCCTTTTCCCTTCGGCCGTGGCGAGCCCCTGAA

Reverse complement sequence

TTCAGGGGCTCGCCACGGCCGAAGGGAAAAGGAAAGAGAGATAAGGGAGAGATGAGAGGAAGGAGGAAGAAGTGTTAAAAGAGAGGATGATACGTGGCCC[T/C]
ATAATATTCTTTTTGACGGATAAATGGGTCACACATATTCTTTTAATTTTAATGTCACATAAACGCCACGTAAAATGAAGACTAAGTCAACACTATCGGT

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 59.50% 37.30% 0.02% 3.24% NA
All Indica  2759 92.50% 5.00% 0.04% 2.39% NA
All Japonica  1512 5.00% 89.30% 0.00% 5.69% NA
Aus  269 52.00% 48.00% 0.00% 0.00% NA
Indica I  595 99.00% 1.00% 0.00% 0.00% NA
Indica II  465 85.20% 4.70% 0.22% 9.89% NA
Indica III  913 93.00% 6.60% 0.00% 0.44% NA
Indica Intermediate  786 91.50% 6.50% 0.00% 2.04% NA
Temperate Japonica  767 0.30% 98.70% 0.00% 1.04% NA
Tropical Japonica  504 13.70% 82.70% 0.00% 3.57% NA
Japonica Intermediate  241 2.10% 73.00% 0.00% 24.90% NA
VI/Aromatic  96 2.10% 97.90% 0.00% 0.00% NA
Intermediate  90 43.30% 55.60% 0.00% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0118657999 A -> G LOC_Os01g33930.1 upstream_gene_variant ; 1095.0bp to feature; MODIFIER silent_mutation Average:89.284; most accessible tissue: Callus, score: 95.952 N N N N
vg0118657999 A -> G LOC_Os01g33920.1 downstream_gene_variant ; 404.0bp to feature; MODIFIER silent_mutation Average:89.284; most accessible tissue: Callus, score: 95.952 N N N N
vg0118657999 A -> G LOC_Os01g33910-LOC_Os01g33920 intergenic_region ; MODIFIER silent_mutation Average:89.284; most accessible tissue: Callus, score: 95.952 N N N N
vg0118657999 A -> DEL N N silent_mutation Average:89.284; most accessible tissue: Callus, score: 95.952 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)
vg0118657999 A G -0.13 -0.1 -0.07 -0.08 -0.07 -0.08

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0118657999 NA 1.18E-44 mr1092 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
vg0118657999 9.81E-06 2.81E-51 mr1154 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
vg0118657999 1.50E-06 1.08E-41 mr1200 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
vg0118657999 NA 2.38E-15 mr1228 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
vg0118657999 NA 1.02E-48 mr1519 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
vg0118657999 NA 6.18E-23 mr1571 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
vg0118657999 NA 5.86E-21 mr1698 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
vg0118657999 NA 4.10E-48 mr1519_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
vg0118657999 NA 7.01E-14 mr1575_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
vg0118657999 NA 1.71E-23 mr1698_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
vg0118657999 NA 8.28E-17 mr1712_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
vg0118657999 NA 2.35E-47 mr1861_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