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Detailed information for vg0909322986:

Variant ID: vg0909322986 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 9322986
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:


CAATGCTGACACCGTTGCCTCCTGATCCGTCGTAGGATCTGTAGCTGACGCCACCCCACCAGCCACCGTAGCCACCGGATCCGCCGCAAGATCCATCGCT[G/A]
GCGCCAACCCGCCCGCCACCGATGCCGCCGACACTGGATCTGCTGTGGGAGTCAACGTTGCGCCTGACGCAGCTTCGCCTGTTGTCACCATCTCTTGGCC

Reverse complement sequence

GGCCAAGAGATGGTGACAACAGGCGAAGCTGCGTCAGGCGCAACGTTGACTCCCACAGCAGATCCAGTGTCGGCGGCATCGGTGGCGGGCGGGTTGGCGC[C/T]
AGCGATGGATCTTGCGGCGGATCCGGTGGCTACGGTGGCTGGTGGGGTGGCGTCAGCTACAGATCCTACGACGGATCAGGAGGCAACGGTGTCAGCATTG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 51.40% 48.20% 0.40% 0.00% NA
All Indica  2759 30.40% 69.00% 0.54% 0.00% NA
All Japonica  1512 77.30% 22.60% 0.13% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 24.40% 74.30% 1.34% 0.00% NA
Indica II  465 18.50% 81.50% 0.00% 0.00% NA
Indica III  913 42.30% 57.40% 0.33% 0.00% NA
Indica Intermediate  786 28.20% 71.20% 0.51% 0.00% NA
Temperate Japonica  767 87.10% 12.80% 0.13% 0.00% NA
Tropical Japonica  504 70.80% 29.20% 0.00% 0.00% NA
Japonica Intermediate  241 59.80% 39.80% 0.41% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 66.70% 31.10% 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
vg0909322986 G -> A LOC_Os09g15284.1 upstream_gene_variant ; 973.0bp to feature; MODIFIER silent_mutation Average:75.861; most accessible tissue: Minghui63 young leaf, score: 88.753 N N N N
vg0909322986 G -> A LOC_Os09g15290.1 upstream_gene_variant ; 5.0bp to feature; MODIFIER silent_mutation Average:75.861; most accessible tissue: Minghui63 young leaf, score: 88.753 N N N N
vg0909322986 G -> A LOC_Os09g15300.1 downstream_gene_variant ; 3018.0bp to feature; MODIFIER silent_mutation Average:75.861; most accessible tissue: Minghui63 young leaf, score: 88.753 N N N N
vg0909322986 G -> A LOC_Os09g15290-LOC_Os09g15300 intergenic_region ; MODIFIER silent_mutation Average:75.861; most accessible tissue: Minghui63 young leaf, score: 88.753 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)
vg0909322986 G A -0.01 -0.01 -0.01 -0.02 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0909322986 NA 3.37E-06 mr1111 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
vg0909322986 5.89E-07 NA mr1133_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
vg0909322986 NA 8.50E-07 mr1263_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
vg0909322986 NA 6.61E-07 mr1834_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