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Detailed information for vg0334690605:

Variant ID: vg0334690605 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 34690605
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:


GACGACGGTAGACCTCAGGAGGGCATGATTGGTATCTCTGGTAAGTAGGCTTGCAAGAACTGATCCCTGAAACTTCTTTGCCCTGGCTGGTGGTGCTGAA[C/T]
TGCCTCTTGGCTGCAGGCAATTCCATGGCAAGAAGATCGAGAGGAAAAATTTCTTGGTCTGATTATTGCTTCATCGTTTTTCCTTTGGATGCATAAATAT

Reverse complement sequence

ATATTTATGCATCCAAAGGAAAAACGATGAAGCAATAATCAGACCAAGAAATTTTTCCTCTCGATCTTCTTGCCATGGAATTGCCTGCAGCCAAGAGGCA[G/A]
TTCAGCACCACCAGCCAGGGCAAAGAAGTTTCAGGGATCAGTTCTTGCAAGCCTACTTACCAGAGATACCAATCATGCCCTCCTGAGGTCTACCGTCGTC

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 59.90% 40.10% 0.04% 0.00% NA
All Indica  2759 34.90% 65.00% 0.07% 0.00% NA
All Japonica  1512 99.50% 0.50% 0.00% 0.00% NA
Aus  269 79.20% 20.80% 0.00% 0.00% NA
Indica I  595 8.40% 91.60% 0.00% 0.00% NA
Indica II  465 24.50% 75.30% 0.22% 0.00% NA
Indica III  913 53.90% 46.00% 0.11% 0.00% NA
Indica Intermediate  786 39.10% 60.90% 0.00% 0.00% NA
Temperate Japonica  767 99.60% 0.40% 0.00% 0.00% NA
Tropical Japonica  504 99.40% 0.60% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.80% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 62.20% 37.80% 0.00% 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
vg0334690605 C -> T LOC_Os03g61060.1 synonymous_variant ; p.Gln9Gln; LOW synonymous_codon Average:90.925; most accessible tissue: Minghui63 root, score: 97.339 N N N N
vg0334690605 C -> T LOC_Os03g61060.2 synonymous_variant ; p.Gln9Gln; LOW synonymous_codon Average:90.925; most accessible tissue: Minghui63 root, score: 97.339 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)
vg0334690605 C T -0.1 0.01 0.04 -0.06 -0.05 -0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0334690605 NA 1.78E-06 mr1850 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
vg0334690605 NA 1.16E-07 mr1212_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
vg0334690605 NA 4.35E-10 mr1649_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
vg0334690605 3.53E-07 NA mr1671_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
vg0334690605 2.93E-07 NA mr1671_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
vg0334690605 NA 1.26E-08 mr1798_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