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Detailed information for vg0140618489:

Variant ID: vg0140618489 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 40618489
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:


CGAAGAAGAAGGAGAGATCTGAGCCATCAAGCATGGTGGTGGTGACCTAACTAGAAGCAGCCATTGATGCAAATGCGATGCAATGTAGTAGTGTGATCAT[G/T]
TCACCAAGAAGCTGTCCTAAAGGCTTCACCTACCAACCAATTCTGGTGAGCTCACTGCAGCTGCAAGCAGTTACAGGCAGGCAGGCAGGCAGGTTGGTGG

Reverse complement sequence

CCACCAACCTGCCTGCCTGCCTGCCTGTAACTGCTTGCAGCTGCAGTGAGCTCACCAGAATTGGTTGGTAGGTGAAGCCTTTAGGACAGCTTCTTGGTGA[C/A]
ATGATCACACTACTACATTGCATCGCATTTGCATCAATGGCTGCTTCTAGTTAGGTCACCACCACCATGCTTGATGGCTCAGATCTCTCCTTCTTCTTCG

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 80.20% 19.70% 0.08% 0.00% NA
All Indica  2759 94.70% 5.20% 0.07% 0.00% NA
All Japonica  1512 48.90% 51.10% 0.07% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 92.80% 7.20% 0.00% 0.00% NA
Indica II  465 92.50% 7.50% 0.00% 0.00% NA
Indica III  913 99.50% 0.50% 0.00% 0.00% NA
Indica Intermediate  786 92.10% 7.60% 0.25% 0.00% NA
Temperate Japonica  767 55.00% 44.90% 0.13% 0.00% NA
Tropical Japonica  504 53.80% 46.20% 0.00% 0.00% NA
Japonica Intermediate  241 19.10% 80.90% 0.00% 0.00% NA
VI/Aromatic  96 94.80% 5.20% 0.00% 0.00% NA
Intermediate  90 85.60% 13.30% 1.11% 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
vg0140618489 G -> T LOC_Os01g70180.2 upstream_gene_variant ; 1260.0bp to feature; MODIFIER silent_mutation Average:83.997; most accessible tissue: Zhenshan97 flower, score: 96.218 N N N N
vg0140618489 G -> T LOC_Os01g70180.1 intron_variant ; MODIFIER silent_mutation Average:83.997; most accessible tissue: Zhenshan97 flower, score: 96.218 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)
vg0140618489 G T -0.07 -0.06 -0.02 -0.07 -0.12 -0.13

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0140618489 NA 2.81E-08 mr1691 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
vg0140618489 6.40E-06 NA mr1977 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