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Detailed information for vg0224273930:

Variant ID: vg0224273930 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 24273930
Reference Allele: GAlternative Allele: C
Primary Allele: GSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CCAACTCAAACCCAGCCATCCAGGCATCCCCGAACGCTGCATATGCTGCTGCAGGCGCGGCCACCCGCCGGGCGGTCTGCCGTCTCGCTTCCGCGACGAC[G/C]
TGGCCTTCGCCGTCGACGGTGTTGGGTGTAATCCCACATCGATAATTGACGATAGAGAAACACGACTTAAAAGATAGGAATGATGCTCATCCATCAGACT

Reverse complement sequence

AGTCTGATGGATGAGCATCATTCCTATCTTTTAAGTCGTGTTTCTCTATCGTCAATTATCGATGTGGGATTACACCCAACACCGTCGACGGCGAAGGCCA[C/G]
GTCGTCGCGGAAGCGAGACGGCAGACCGCCCGGCGGGTGGCCGCGCCTGCAGCAGCATATGCAGCGTTCGGGGATGCCTGGATGGCTGGGTTTGAGTTGG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.20% 2.80% 0.02% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 92.10% 7.90% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 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 99.00% 1.00% 0.00% 0.00% NA
Temperate Japonica  767 86.20% 13.70% 0.13% 0.00% NA
Tropical Japonica  504 99.20% 0.80% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 4.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0224273930 G -> C LOC_Os02g40090.1 upstream_gene_variant ; 255.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40100.1 upstream_gene_variant ; 2378.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40090.4 upstream_gene_variant ; 405.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40090.5 upstream_gene_variant ; 369.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40090.3 upstream_gene_variant ; 256.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40080.1 downstream_gene_variant ; 3909.0bp to feature; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 N N N N
vg0224273930 G -> C LOC_Os02g40090-LOC_Os02g40100 intergenic_region ; MODIFIER silent_mutation Average:98.854; most accessible tissue: Zhenshan97 panicle, score: 99.321 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)
vg0224273930 G C -0.03 -0.05 -0.05 -0.04 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0224273930 5.52E-08 1.16E-07 mr1238 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
vg0224273930 7.26E-06 8.46E-07 mr1309 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
vg0224273930 NA 3.44E-06 mr1841 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
vg0224273930 3.24E-07 3.04E-07 mr1900 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
vg0224273930 4.75E-07 1.65E-06 mr1238_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
vg0224273930 1.01E-06 1.01E-06 mr1484_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
vg0224273930 8.11E-06 NA mr1900_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
vg0224273930 8.63E-06 8.63E-06 mr1945_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