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Detailed information for vg0431082926:

Variant ID: vg0431082926 (JBrowse)Variation Type: SNP
Chromosome: chr04Position: 31082926
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.62, T: 0.38, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


GATAAGGAGAAAGTTGTTGACATATGGGTCCCACTCATTACTCAACGAGTCAACCGAGGTTAACTTGTTACTACGTCAGTAGAAACCGTTTCCAAACCAT[C/T]
GAAGGAGCTGATTTGTAGTTGAGAGAGGCTAAGGAGCTGATTTGTTATATTCGGTTTTATAGTTGAGAGAGGCTACTGCTGGGTGGTAACTACTGTCCTC

Reverse complement sequence

GAGGACAGTAGTTACCACCCAGCAGTAGCCTCTCTCAACTATAAAACCGAATATAACAAATCAGCTCCTTAGCCTCTCTCAACTACAAATCAGCTCCTTC[G/A]
ATGGTTTGGAAACGGTTTCTACTGACGTAGTAACAAGTTAACCTCGGTTGACTCGTTGAGTAATGAGTGGGACCCATATGTCAACAACTTTCTCCTTATC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 52.40% 47.30% 0.17% 0.13% NA
All Indica  2759 21.90% 77.60% 0.25% 0.18% NA
All Japonica  1512 97.50% 2.40% 0.00% 0.07% NA
Aus  269 98.50% 1.50% 0.00% 0.00% NA
Indica I  595 15.10% 83.90% 0.34% 0.67% NA
Indica II  465 12.70% 87.30% 0.00% 0.00% NA
Indica III  913 32.00% 67.70% 0.33% 0.00% NA
Indica Intermediate  786 20.90% 78.80% 0.25% 0.13% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 94.80% 5.20% 0.00% 0.00% NA
Japonica Intermediate  241 96.30% 3.30% 0.00% 0.41% NA
VI/Aromatic  96 79.20% 19.80% 1.04% 0.00% NA
Intermediate  90 62.20% 37.80% 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
vg0431082926 C -> DEL N N silent_mutation Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 96.214 N N N N
vg0431082926 C -> T LOC_Os04g52310.1 upstream_gene_variant ; 2368.0bp to feature; MODIFIER silent_mutation Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 96.214 N N N N
vg0431082926 C -> T LOC_Os04g52300.1 downstream_gene_variant ; 4998.0bp to feature; MODIFIER silent_mutation Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 96.214 N N N N
vg0431082926 C -> T LOC_Os04g52310-LOC_Os04g52320 intergenic_region ; MODIFIER silent_mutation Average:89.194; most accessible tissue: Zhenshan97 panicle, score: 96.214 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)
vg0431082926 C T 0.0 -0.02 -0.03 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0431082926 NA 2.15E-20 mr1131 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
vg0431082926 NA 4.60E-07 mr1980 Ind_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