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Detailed information for vg0909170084:

Variant ID: vg0909170084 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9170084
Reference Allele: CAlternative Allele: A
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:


AAACAAAAATTTTCAGCTATATAAAATCAGCCTATGATTCTTCTTTTCATTGGAACAATCAGATTTGCTTCATGAAGAAGGATTTGGTAGAGTTGGACGG[C/A]
CTTGTGGTGCAAGTTTTTTCATTGGCTTGCAGTCATCGCCTTGCCAAGCAAGGGCTGCAACATGATCAGGCCGAAGAATCGATCCAACACATCGTTGTCA

Reverse complement sequence

TGACAACGATGTGTTGGATCGATTCTTCGGCCTGATCATGTTGCAGCCCTTGCTTGGCAAGGCGATGACTGCAAGCCAATGAAAAAACTTGCACCACAAG[G/T]
CCGTCCAACTCTACCAAATCCTTCTTCATGAAGCAAATCTGATTGTTCCAATGAAAAGAAGAATCATAGGCTGATTTTATATAGCTGAAAATTTTTGTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.60% 45.80% 0.11% 2.52% NA
All Indica  2759 76.70% 23.20% 0.04% 0.07% NA
All Japonica  1512 15.00% 81.60% 0.20% 3.17% NA
Aus  269 20.10% 79.60% 0.00% 0.37% NA
Indica I  595 77.80% 22.20% 0.00% 0.00% NA
Indica II  465 87.50% 12.50% 0.00% 0.00% NA
Indica III  913 72.80% 26.90% 0.11% 0.11% NA
Indica Intermediate  786 73.80% 26.10% 0.00% 0.13% NA
Temperate Japonica  767 14.30% 81.50% 0.39% 3.78% NA
Tropical Japonica  504 8.70% 88.50% 0.00% 2.78% NA
Japonica Intermediate  241 30.30% 67.60% 0.00% 2.07% NA
VI/Aromatic  96 19.80% 17.70% 0.00% 62.50% NA
Intermediate  90 26.70% 63.30% 1.11% 8.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0909170084 C -> DEL N N silent_mutation Average:77.114; most accessible tissue: Zhenshan97 young leaf, score: 96.752 N N N N
vg0909170084 C -> A LOC_Os09g15100-LOC_Os09g15120 intergenic_region ; MODIFIER silent_mutation Average:77.114; most accessible tissue: Zhenshan97 young leaf, score: 96.752 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)
vg0909170084 C A -0.03 0.09 0.04 -0.05 -0.06 -0.11

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909170084 NA 7.63E-06 mr1306 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
vg0909170084 4.56E-06 4.56E-06 mr1501 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