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Detailed information for vg0336048686:

Variant ID: vg0336048686 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 36048686
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TATAAACATATTTTAAAAAGATAAAAGAGAAGATAGAAGAGCAGCGGGCTATAGATATGTAGCCAGCTGCAGCACGGATTTCAAGACATAATGTGTACGT[G/A]
TATGACAGATGGGACCAGGTATTAATAGTATAGTAAGCAACTATTGTATGAATTAGCTATTAAATTGGCTATAGATGATTTGGAGCTAGTAGTTGGCTAT

Reverse complement sequence

ATAGCCAACTACTAGCTCCAAATCATCTATAGCCAATTTAATAGCTAATTCATACAATAGTTGCTTACTATACTATTAATACCTGGTCCCATCTGTCATA[C/T]
ACGTACACATTATGTCTTGAAATCCGTGCTGCAGCTGGCTACATATCTATAGCCCGCTGCTCTTCTATCTTCTCTTTTATCTTTTTAAAATATGTTTATA

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 94.70% 5.20% 0.04% 0.00% NA
All Indica  2759 91.20% 8.80% 0.07% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 96.50% 3.50% 0.00% 0.00% NA
Indica II  465 95.30% 4.70% 0.00% 0.00% NA
Indica III  913 84.90% 14.90% 0.22% 0.00% NA
Indica Intermediate  786 92.00% 8.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0336048686 G -> A LOC_Os03g63820.1 upstream_gene_variant ; 2846.0bp to feature; MODIFIER silent_mutation Average:67.75; most accessible tissue: Zhenshan97 flower, score: 86.702 N N N N
vg0336048686 G -> A LOC_Os03g63810.1 downstream_gene_variant ; 4864.0bp to feature; MODIFIER silent_mutation Average:67.75; most accessible tissue: Zhenshan97 flower, score: 86.702 N N N N
vg0336048686 G -> A LOC_Os03g63810-LOC_Os03g63820 intergenic_region ; MODIFIER silent_mutation Average:67.75; most accessible tissue: Zhenshan97 flower, score: 86.702 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)
vg0336048686 G A -0.04 -0.01 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0336048686 NA 7.00E-06 mr1165 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
vg0336048686 NA 3.56E-06 mr1291 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
vg0336048686 3.82E-06 3.06E-06 mr1471 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
vg0336048686 2.31E-06 2.04E-06 mr1479 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
vg0336048686 NA 4.59E-06 mr1522 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
vg0336048686 2.87E-06 7.44E-08 mr1553 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
vg0336048686 5.77E-08 3.76E-08 mr1892 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