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Detailed information for vg0824712199:

Variant ID: vg0824712199 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24712199
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTGAAACTGGCTAGTGCCACTAGTTTGTGAAAAAATGGTTTAGATCCAATAGCAAAATATCTCAGCACAAATCTTAGCACGGGATCCACGGGCCAAAAA[G/A]
AAATTTAACAGTCCTGAGAACTGCCCACAACTAGCTAGAAAAAAAAAAGCGGCCGTAACCTTGACTTGTGAGAGCACTGAGCAAAAAAAGAGAGAGAGAG

Reverse complement sequence

CTCTCTCTCTCTTTTTTTGCTCAGTGCTCTCACAAGTCAAGGTTACGGCCGCTTTTTTTTTTCTAGCTAGTTGTGGGCAGTTCTCAGGACTGTTAAATTT[C/T]
TTTTTGGCCCGTGGATCCCGTGCTAAGATTTGTGCTGAGATATTTTGCTATTGGATCTAAACCATTTTTTCACAAACTAGTGGCACTAGCCAGTTTCACC

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 78.80% 19.90% 1.25% 0.00% NA
All Indica  2759 94.80% 5.00% 0.22% 0.00% NA
All Japonica  1512 45.60% 51.20% 3.24% 0.00% NA
Aus  269 95.20% 4.50% 0.37% 0.00% NA
Indica I  595 96.60% 3.00% 0.34% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 91.90% 8.00% 0.11% 0.00% NA
Indica Intermediate  786 93.90% 5.70% 0.38% 0.00% NA
Temperate Japonica  767 33.20% 61.00% 5.74% 0.00% NA
Tropical Japonica  504 66.10% 33.10% 0.79% 0.00% NA
Japonica Intermediate  241 41.90% 57.70% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 20.00% 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
vg0824712199 G -> A LOC_Os08g39120.1 upstream_gene_variant ; 226.0bp to feature; MODIFIER silent_mutation Average:87.12; most accessible tissue: Callus, score: 98.163 N N N N
vg0824712199 G -> A LOC_Os08g39130.1 upstream_gene_variant ; 4114.0bp to feature; MODIFIER silent_mutation Average:87.12; most accessible tissue: Callus, score: 98.163 N N N N
vg0824712199 G -> A LOC_Os08g39100-LOC_Os08g39120 intergenic_region ; MODIFIER silent_mutation Average:87.12; most accessible tissue: Callus, score: 98.163 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)
vg0824712199 G A -0.04 -0.04 -0.04 -0.03 -0.05 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824712199 NA 8.97E-09 mr1137 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
vg0824712199 NA 3.38E-06 mr1164 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
vg0824712199 NA 2.56E-06 mr1183 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
vg0824712199 NA 1.12E-06 mr1202 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
vg0824712199 NA 3.06E-08 mr1617 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
vg0824712199 NA 6.00E-08 mr1627 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
vg0824712199 NA 7.37E-08 mr1137_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
vg0824712199 NA 1.59E-06 mr1161_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
vg0824712199 NA 5.89E-07 mr1164_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
vg0824712199 NA 9.09E-06 mr1617_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
vg0824712199 NA 2.41E-10 mr1627_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