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Detailed information for vg1103859312:

Variant ID: vg1103859312 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 3859312
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCAGCTGATCAATCGATCATATATAGCCTCATAGATTGGGGATGCCGGATGATGCGTGCGTCTGCAAAATGAGCGAACGTCACGCATCCAATGCAATGC[G/A]
TCCAGGCCGGTCAGCCAGCAGCAGCAGCAGCAGATAGCAGCTACCCCCAACCGTTTCAAGCTTCGCCGGTTTTCAGACTCTGATAGACCAAGTCTGGGGG

Reverse complement sequence

CCCCCAGACTTGGTCTATCAGAGTCTGAAAACCGGCGAAGCTTGAAACGGTTGGGGGTAGCTGCTATCTGCTGCTGCTGCTGCTGGCTGACCGGCCTGGA[C/T]
GCATTGCATTGGATGCGTGACGTTCGCTCATTTTGCAGACGCACGCATCATCCGGCATCCCCAATCTATGAGGCTATATATGATCGATTGATCAGCTGGC

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 92.80% 3.90% 3.26% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 77.90% 11.90% 10.19% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 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 58.90% 22.80% 18.25% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 92.10% 2.10% 5.81% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1103859312 G -> A LOC_Os11g07600.1 upstream_gene_variant ; 2030.0bp to feature; MODIFIER silent_mutation Average:79.256; most accessible tissue: Minghui63 panicle, score: 96.207 N N N N
vg1103859312 G -> A LOC_Os11g07600-LOC_Os11g07620 intergenic_region ; MODIFIER silent_mutation Average:79.256; most accessible tissue: Minghui63 panicle, score: 96.207 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)
vg1103859312 G A -0.07 -0.05 -0.04 -0.07 -0.05 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1103859312 NA 9.71E-08 mr1229 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
vg1103859312 1.73E-06 1.73E-06 mr1728 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