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Detailed information for vg0106766299:

Variant ID: vg0106766299 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 6766299
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACCAGCTATAAACATATTTTAAAGAGATAAAGGAAGAGAGAGAGAGGAGCAGCGGACTACAGATCTGTAGCCAGCTGCAGCACAGACTCCAAAACGTAAT[G/A]
TGGTATGATATGTGAGACCATGTATTAATAGTATATAAAGCAACTATTGTATGAATTGGCTATTATATTAGCTATAGATGATTTGAAGCTAGTAGTTGGC

Reverse complement sequence

GCCAACTACTAGCTTCAAATCATCTATAGCTAATATAATAGCCAATTCATACAATAGTTGCTTTATATACTATTAATACATGGTCTCACATATCATACCA[C/T]
ATTACGTTTTGGAGTCTGTGCTGCAGCTGGCTACAGATCTGTAGTCCGCTGCTCCTCTCTCTCTCTTCCTTTATCTCTTTAAAATATGTTTATAGCTGGT

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 95.30% 3.70% 0.99% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 86.40% 10.60% 2.98% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.00% 0.11% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 90.70% 4.30% 4.95% 0.00% NA
Tropical Japonica  504 85.90% 13.90% 0.20% 0.00% NA
Japonica Intermediate  241 73.40% 24.10% 2.49% 0.00% NA
VI/Aromatic  96 90.60% 9.40% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0106766299 G -> A LOC_Os01g12381.1 upstream_gene_variant ; 411.0bp to feature; MODIFIER silent_mutation Average:87.876; most accessible tissue: Zhenshan97 root, score: 97.61 N N N N
vg0106766299 G -> A LOC_Os01g12390.1 downstream_gene_variant ; 198.0bp to feature; MODIFIER silent_mutation Average:87.876; most accessible tissue: Zhenshan97 root, score: 97.61 N N N N
vg0106766299 G -> A LOC_Os01g12381-LOC_Os01g12390 intergenic_region ; MODIFIER silent_mutation Average:87.876; most accessible tissue: Zhenshan97 root, score: 97.61 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)
vg0106766299 G A 0.01 0.0 0.0 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0106766299 4.44E-06 NA mr1201 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
vg0106766299 5.85E-06 NA mr1201 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