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Detailed information for vg0922156063:

Variant ID: vg0922156063 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 22156063
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.01, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:


ACTTATGACTAATTATAGACTAATTAAGTTCAAAAGATTCGTCTCGCGATTTATGTAAACTGTGCAATTAGTTTTTTTAATCTATATTTAATGCTCCATG[C/A]
ATATGTCCAAAGATTCGAAGTGACGTTTTTTTGGCAAATTTATTTGAAAACTAAACAAGGCCTTAGGCTTAACACTATGAACAACGGCGTGCTATTAGGA

Reverse complement sequence

TCCTAATAGCACGCCGTTGTTCATAGTGTTAAGCCTAAGGCCTTGTTTAGTTTTCAAATAAATTTGCCAAAAAAACGTCACTTCGAATCTTTGGACATAT[G/T]
CATGGAGCATTAAATATAGATTAAAAAAACTAATTGCACAGTTTACATAAATCGCGAGACGAATCTTTTGAACTTAATTAGTCTATAATTAGTCATAAGT

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 55.80% 40.40% 0.17% 3.66% NA
All Indica  2759 28.40% 65.10% 0.29% 6.20% NA
All Japonica  1512 99.70% 0.30% 0.00% 0.07% NA
Aus  269 67.30% 32.70% 0.00% 0.00% NA
Indica I  595 41.80% 57.30% 0.00% 0.84% NA
Indica II  465 22.20% 75.90% 0.22% 1.72% NA
Indica III  913 23.50% 64.60% 0.33% 11.50% NA
Indica Intermediate  786 27.50% 65.30% 0.51% 6.74% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.00% 0.00% 0.20% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 80.00% 18.90% 0.00% 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
vg0922156063 C -> DEL N N silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38500.1 upstream_gene_variant ; 454.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38500.2 upstream_gene_variant ; 454.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38500.3 upstream_gene_variant ; 454.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38490.1 downstream_gene_variant ; 4247.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38510.1 downstream_gene_variant ; 863.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38520.1 downstream_gene_variant ; 4814.0bp to feature; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 N N N N
vg0922156063 C -> A LOC_Os09g38500-LOC_Os09g38510 intergenic_region ; MODIFIER silent_mutation Average:75.637; most accessible tissue: Callus, score: 90.815 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)
vg0922156063 C A -0.01 -0.01 -0.01 -0.01 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0922156063 2.80E-18 NA mr1865 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
vg0922156063 1.92E-16 1.02E-16 mr1865 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
vg0922156063 NA 1.43E-06 mr1629_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
vg0922156063 1.81E-13 NA mr1865_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
vg0922156063 2.49E-13 1.05E-14 mr1865_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