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Detailed information for vg0123658384:

Variant ID: vg0123658384 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 23658384
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.78, A: 0.22, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:


TCCCTCCAGCGTGGCTGCTTCACATGAGCTCATGATGAATCAGCGGCTACGGGACGGGAGGACTTTAGGGTTTCGGAGGCGGAGGCGGCGGCGGCCGAGG[G/A]
AGAGGGATCGCTTTGGTGGAGGATTTCTTAGGGTTTGCGAAGGCCGACGCTTTCGGGCGGGGGAAAGTGGACATGTTAACGTTGAAGGAATAGTTCATTT

Reverse complement sequence

AAATGAACTATTCCTTCAACGTTAACATGTCCACTTTCCCCCGCCCGAAAGCGTCGGCCTTCGCAAACCCTAAGAAATCCTCCACCAAAGCGATCCCTCT[C/T]
CCTCGGCCGCCGCCGCCTCCGCCTCCGAAACCCTAAAGTCCTCCCGTCCCGTAGCCGCTGATTCATCATGAGCTCATGTGAAGCAGCCACGCTGGAGGGA

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 67.70% 30.80% 0.55% 0.89% NA
All Indica  2759 91.10% 7.80% 0.80% 0.33% NA
All Japonica  1512 18.00% 79.60% 0.26% 2.12% NA
Aus  269 98.10% 1.90% 0.00% 0.00% NA
Indica I  595 96.60% 2.70% 0.67% 0.00% NA
Indica II  465 96.30% 3.20% 0.22% 0.22% NA
Indica III  913 84.20% 13.90% 1.10% 0.77% NA
Indica Intermediate  786 91.90% 7.10% 0.89% 0.13% NA
Temperate Japonica  767 0.70% 94.80% 0.39% 4.17% NA
Tropical Japonica  504 42.30% 57.50% 0.20% 0.00% NA
Japonica Intermediate  241 22.40% 77.60% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 65.60% 33.30% 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
vg0123658384 G -> A LOC_Os01g41790.1 upstream_gene_variant ; 68.0bp to feature; MODIFIER silent_mutation Average:81.74; most accessible tissue: Zhenshan97 flower, score: 91.056 N N N N
vg0123658384 G -> A LOC_Os01g41800.1 downstream_gene_variant ; 4675.0bp to feature; MODIFIER silent_mutation Average:81.74; most accessible tissue: Zhenshan97 flower, score: 91.056 N N N N
vg0123658384 G -> A LOC_Os01g41790-LOC_Os01g41800 intergenic_region ; MODIFIER silent_mutation Average:81.74; most accessible tissue: Zhenshan97 flower, score: 91.056 N N N N
vg0123658384 G -> DEL N N silent_mutation Average:81.74; most accessible tissue: Zhenshan97 flower, score: 91.056 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)
vg0123658384 G A -0.02 -0.02 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0123658384 2.81E-06 NA mr1023_2 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
vg0123658384 NA 4.88E-06 mr1289_2 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
vg0123658384 NA 3.54E-06 mr1359_2 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
vg0123658384 NA 3.86E-09 mr1363_2 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
vg0123658384 NA 5.34E-06 mr1596_2 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