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Detailed information for vg0202216666:

Variant ID: vg0202216666 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 2216666
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AATTTAAGAAGATAAATAAGAAGAGAAAAGAGCAGCGGGCTATATATTTATAGCCAGCTGTAGCACAGATTTCAAGACGCAGTGTGTGTATGACAGGTGG[G/A]
ACCAGGTATTAATAGTGTAGTATGTAACTATTGTATGGATAAGCTATTAGATTGGTTATAGATAAATTAAAGCTAGTAGTTGGCTTGGATAAGCTATTAG

Reverse complement sequence

CTAATAGCTTATCCAAGCCAACTACTAGCTTTAATTTATCTATAACCAATCTAATAGCTTATCCATACAATAGTTACATACTACACTATTAATACCTGGT[C/T]
CCACCTGTCATACACACACTGCGTCTTGAAATCTGTGCTACAGCTGGCTATAAATATATAGCCCGCTGCTCTTTTCTCTTCTTATTTATCTTCTTAAATT

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 98.40% 1.10% 0.44% 0.00% NA
All Indica  2759 99.90% 0.10% 0.04% 0.00% NA
All Japonica  1512 95.80% 3.10% 1.12% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.20% 0.22% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 88.30% 8.50% 3.17% 0.00% NA
Japonica Intermediate  241 97.90% 1.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 93.30% 3.30% 3.33% 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
vg0202216666 G -> A LOC_Os02g04810.1 upstream_gene_variant ; 2034.0bp to feature; MODIFIER silent_mutation Average:63.273; most accessible tissue: Zhenshan97 root, score: 91.257 N N N N
vg0202216666 G -> A LOC_Os02g04810-LOC_Os02g04820 intergenic_region ; MODIFIER silent_mutation Average:63.273; most accessible tissue: Zhenshan97 root, score: 91.257 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)
vg0202216666 G A -0.06 -0.06 -0.02 -0.05 -0.04 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0202216666 NA 4.72E-06 mr1448 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
vg0202216666 NA 1.33E-06 mr1188_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
vg0202216666 2.49E-07 2.49E-07 mr1448_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