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Detailed information for vg0227468030:

Variant ID: vg0227468030 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 27468030
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


TGCAACTGTGTAGTAGTAGGCGCTAGCAGTGCTTATAACTGTATAAACAGCCAAAAAGAGGCCATAACGGCGCAACGAGCACTAGCAAATCTCAGGGCAC[C/T]
ACAATGGTTATCTATAAACTCTCTATAAGAGATTTATGTCAGCATATTTTTCTACTTAGAAGATATTAAAGAGAGAGAGAGAGCAAATCTATCTACTAAC

Reverse complement sequence

GTTAGTAGATAGATTTGCTCTCTCTCTCTCTTTAATATCTTCTAAGTAGAAAAATATGCTGACATAAATCTCTTATAGAGAGTTTATAGATAACCATTGT[G/A]
GTGCCCTGAGATTTGCTAGTGCTCGTTGCGCCGTTATGGCCTCTTTTTGGCTGTTTATACAGTTATAAGCACTGCTAGCGCCTACTACTACACAGTTGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.20% 17.20% 2.62% 0.00% NA
All Indica  2759 98.00% 1.60% 0.33% 0.00% NA
All Japonica  1512 46.40% 46.30% 7.28% 0.00% NA
Aus  269 99.30% 0.00% 0.74% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 96.30% 3.00% 0.65% 0.00% NA
Indica III  913 98.40% 1.50% 0.11% 0.00% NA
Indica Intermediate  786 97.60% 1.80% 0.64% 0.00% NA
Temperate Japonica  767 58.70% 31.90% 9.39% 0.00% NA
Tropical Japonica  504 36.30% 60.50% 3.17% 0.00% NA
Japonica Intermediate  241 28.60% 62.20% 9.13% 0.00% NA
VI/Aromatic  96 52.10% 46.90% 1.04% 0.00% NA
Intermediate  90 74.40% 23.30% 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
vg0227468030 C -> T LOC_Os02g45220-LOC_Os02g45225 intergenic_region ; MODIFIER silent_mutation Average:62.982; most accessible tissue: Callus, score: 92.203 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)
vg0227468030 C T -0.02 -0.07 -0.04 -0.01 -0.04 -0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0227468030 NA 2.83E-06 mr1269_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
vg0227468030 NA 1.38E-06 mr1289_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
vg0227468030 NA 9.11E-07 mr1479_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
vg0227468030 4.36E-06 4.36E-06 mr1494_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
vg0227468030 NA 3.84E-12 mr1641_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
vg0227468030 NA 1.97E-08 mr1683_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
vg0227468030 NA 3.69E-06 mr1683_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
vg0227468030 NA 5.10E-06 mr1687_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
vg0227468030 NA 4.41E-06 mr1706_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
vg0227468030 NA 4.63E-06 mr1706_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
vg0227468030 NA 3.12E-06 mr1894_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
vg0227468030 NA 1.96E-07 mr1921_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
vg0227468030 NA 5.55E-06 mr1977_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