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Detailed information for vg0208759843:

Variant ID: vg0208759843 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8759843
Reference Allele: AAlternative Allele: G
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, G: 0.02, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:


TTGTCGGTAATATGTGAGCCGAAGTCACGTAACTTCGACTGCAGATGATCCTGATTCGAACCAGACGTGCCCTAAACTCCTGAATAATCATTATTATAAG[A/G]
AAAGAAAAAAAAGAATTCCTAGAAACCGGGGCCATTTCTAGCGGAGAGGAGGCAGGGTCCCCGGGGTCCACCCATACGCCACAGGGGAATCTGCCCACAC

Reverse complement sequence

GTGTGGGCAGATTCCCCTGTGGCGTATGGGTGGACCCCGGGGACCCTGCCTCCTCTCCGCTAGAAATGGCCCCGGTTTCTAGGAATTCTTTTTTTTCTTT[T/C]
CTTATAATAATGATTATTCAGGAGTTTAGGGCACGTCTGGTTCGAATCAGGATCATCTGCAGTCGAAGTTACGTGACTTCGGCTCACATATTACCGACAA

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 67.70% 21.50% 6.12% 4.74% NA
All Indica  2759 56.40% 32.10% 5.69% 5.80% NA
All Japonica  1512 93.50% 6.20% 0.33% 0.00% NA
Aus  269 36.10% 0.00% 41.64% 22.30% NA
Indica I  595 53.60% 29.20% 4.20% 12.94% NA
Indica II  465 80.60% 9.50% 6.45% 3.44% NA
Indica III  913 41.30% 49.30% 5.59% 3.83% NA
Indica Intermediate  786 61.60% 27.90% 6.49% 4.07% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 88.90% 11.10% 0.00% 0.00% NA
Japonica Intermediate  241 90.00% 7.90% 2.07% 0.00% NA
VI/Aromatic  96 65.60% 22.90% 8.33% 3.12% NA
Intermediate  90 77.80% 13.30% 7.78% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0208759843 A -> G LOC_Os02g15594.1 upstream_gene_variant ; 159.0bp to feature; MODIFIER silent_mutation Average:97.479; most accessible tissue: Minghui63 root, score: 98.676 N N N N
vg0208759843 A -> G LOC_Os02g15580.3 upstream_gene_variant ; 3802.0bp to feature; MODIFIER silent_mutation Average:97.479; most accessible tissue: Minghui63 root, score: 98.676 N N N N
vg0208759843 A -> G LOC_Os02g15580.2 upstream_gene_variant ; 3802.0bp to feature; MODIFIER silent_mutation Average:97.479; most accessible tissue: Minghui63 root, score: 98.676 N N N N
vg0208759843 A -> G LOC_Os02g15580-LOC_Os02g15594 intergenic_region ; MODIFIER silent_mutation Average:97.479; most accessible tissue: Minghui63 root, score: 98.676 N N N N
vg0208759843 A -> DEL N N silent_mutation Average:97.479; most accessible tissue: Minghui63 root, score: 98.676 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)
vg0208759843 A G 0.04 0.06 0.05 0.0 0.02 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208759843 NA 1.78E-06 mr1579 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
vg0208759843 5.40E-06 8.36E-07 mr1762 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
vg0208759843 5.17E-06 5.17E-06 mr1762 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