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Detailed information for vg0230321839:

Variant ID: vg0230321839 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 30321839
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.82, T: 0.18, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:


TTGCAATTGCAGCTGGACCTTGGATGCAAACTACTATCACCAAATATGACTAGGGGGTGTTTGGGAGTTAGGGACTAAACTTTAGTCCCTCTCACAAAAG[C/T]
ATAAGTCCCTCAGTTTAGCCCCTCTCTTCCAAACAGGCCCTAGCTAACCTAGCTTTCATTATCTAAAAAAAAAAGCTAACCTAGCTTTTATCTTGGCAAA

Reverse complement sequence

TTTGCCAAGATAAAAGCTAGGTTAGCTTTTTTTTTTAGATAATGAAAGCTAGGTTAGCTAGGGCCTGTTTGGAAGAGAGGGGCTAAACTGAGGGACTTAT[G/A]
CTTTTGTGAGAGGGACTAAAGTTTAGTCCCTAACTCCCAAACACCCCCTAGTCATATTTGGTGATAGTAGTTTGCATCCAAGGTCCAGCTGCAATTGCAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.30% 44.60% 0.04% 0.00% NA
All Indica  2759 83.00% 17.00% 0.00% 0.00% NA
All Japonica  1512 11.70% 88.30% 0.00% 0.00% NA
Aus  269 4.50% 95.50% 0.00% 0.00% NA
Indica I  595 92.60% 7.40% 0.00% 0.00% NA
Indica II  465 94.20% 5.80% 0.00% 0.00% NA
Indica III  913 75.40% 24.60% 0.00% 0.00% NA
Indica Intermediate  786 78.00% 22.00% 0.00% 0.00% NA
Temperate Japonica  767 20.90% 79.10% 0.00% 0.00% NA
Tropical Japonica  504 0.20% 99.80% 0.00% 0.00% NA
Japonica Intermediate  241 6.60% 93.40% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 50.00% 47.80% 2.22% 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
vg0230321839 C -> T LOC_Os02g49600.1 upstream_gene_variant ; 1898.0bp to feature; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0230321839 C -> T LOC_Os02g49620.1 upstream_gene_variant ; 3945.0bp to feature; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0230321839 C -> T LOC_Os02g49610.1 downstream_gene_variant ; 1401.0bp to feature; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0230321839 C -> T LOC_Os02g49610.2 downstream_gene_variant ; 1401.0bp to feature; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0230321839 C -> T LOC_Os02g49610.3 downstream_gene_variant ; 1401.0bp to feature; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 N N N N
vg0230321839 C -> T LOC_Os02g49600-LOC_Os02g49610 intergenic_region ; MODIFIER silent_mutation Average:84.107; most accessible tissue: Zhenshan97 panicle, score: 93.133 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)
vg0230321839 C T 0.0 0.01 -0.01 0.0 -0.01 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0230321839 NA 3.04E-08 mr1260 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
vg0230321839 NA 5.27E-08 mr1798 Ind_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
vg0230321839 NA 1.53E-17 mr1870 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
vg0230321839 NA 1.09E-34 mr1161_2 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
vg0230321839 NA 8.32E-17 mr1180_2 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
vg0230321839 NA 2.68E-22 mr1183_2 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
vg0230321839 NA 5.47E-06 mr1364_2 Ind_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
vg0230321839 NA 5.26E-11 mr1798_2 Ind_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
vg0230321839 NA 8.43E-24 mr1870_2 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