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Detailed information for vg0433052397:

Variant ID: vg0433052397 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 33052397
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TACTAGTAGCTTTAAAGATAAACAAACAAGTGCAGCGGCATGAGTTGATTGATTCCTCATCTGGTGCCGCTATATAATAAGCGAGCGAGATAGGGGTGGA[A/G]
TTGGGGGCGTGGTGGGGGAGTAGCGGTGAGAGCGACCGGGGCGATGAGAGGAGGGACAGAGTGGATAATGCTCGTGCTCTGGAATTCCACTGCCGACTCC

Reverse complement sequence

GGAGTCGGCAGTGGAATTCCAGAGCACGAGCATTATCCACTCTGTCCCTCCTCTCATCGCCCCGGTCGCTCTCACCGCTACTCCCCCACCACGCCCCCAA[T/C]
TCCACCCCTATCTCGCTCGCTTATTATATAGCGGCACCAGATGAGGAATCAATCAACTCATGCCGCTGCACTTGTTTGTTTATCTTTAAAGCTACTAGTA

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 93.90% 6.00% 0.13% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 92.50% 7.10% 0.33% 0.00% NA
Aus  269 39.80% 59.90% 0.37% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 98.40% 1.60% 0.00% 0.00% NA
Tropical Japonica  504 92.30% 7.50% 0.20% 0.00% NA
Japonica Intermediate  241 74.30% 24.10% 1.66% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0433052397 A -> G LOC_Os04g55550.1 upstream_gene_variant ; 639.0bp to feature; MODIFIER silent_mutation Average:99.463; most accessible tissue: Minghui63 root, score: 99.973 N N N N
vg0433052397 A -> G LOC_Os04g55540-LOC_Os04g55550 intergenic_region ; MODIFIER silent_mutation Average:99.463; most accessible tissue: Minghui63 root, score: 99.973 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)
vg0433052397 A G 0.03 0.04 0.0 0.07 0.03 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0433052397 5.44E-06 NA mr1550 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
vg0433052397 3.36E-06 NA mr1550 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
vg0433052397 4.24E-06 NA mr1962_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