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Detailed information for vg0208018838:

Variant ID: vg0208018838 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 8018838
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:


GCCGCTCATCTCCAGCCCGGCGGCGAGCTCGGCCGTCTGCTCCACGGACAGCGCGCCGCCGGAGCCGAAGGAGACGTACACCACCGACCCCGCCGGCTGG[T/C]
GGTCCAGCCACTCCAAGCACGCCGACTCGTCGGGGTCCTCGTTGGAGTTCGGCCGGACGAACGGCCCGACGAGGTACACCGGCGGGAACGCGCCGTTCTC

Reverse complement sequence

GAGAACGGCGCGTTCCCGCCGGTGTACCTCGTCGGGCCGTTCGTCCGGCCGAACTCCAACGAGGACCCCGACGAGTCGGCGTGCTTGGAGTGGCTGGACC[A/G]
CCAGCCGGCGGGGTCGGTGGTGTACGTCTCCTTCGGCTCCGGCGGCGCGCTGTCCGTGGAGCAGACGGCCGAGCTCGCCGCCGGGCTGGAGATGAGCGGC

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 50.70% 49.30% 0.04% 0.00% NA
All Indica  2759 72.30% 27.70% 0.04% 0.00% NA
All Japonica  1512 2.10% 97.90% 0.00% 0.00% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 67.20% 32.80% 0.00% 0.00% NA
Indica II  465 87.50% 12.30% 0.22% 0.00% NA
Indica III  913 66.40% 33.60% 0.00% 0.00% NA
Indica Intermediate  786 73.90% 26.10% 0.00% 0.00% NA
Temperate Japonica  767 1.60% 98.40% 0.00% 0.00% NA
Tropical Japonica  504 2.20% 97.80% 0.00% 0.00% NA
Japonica Intermediate  241 3.30% 96.70% 0.00% 0.00% NA
VI/Aromatic  96 58.30% 41.70% 0.00% 0.00% NA
Intermediate  90 54.40% 44.40% 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
vg0208018838 T -> C LOC_Os02g14540.1 missense_variant ; p.His173Arg; MODERATE nonsynonymous_codon ; H173R Average:84.681; most accessible tissue: Minghui63 flag leaf, score: 95.024 benign -0.457 TOLERATED 0.93

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)
vg0208018838 T C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0208018838 NA 5.35E-06 mr1171 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
vg0208018838 NA 2.15E-09 mr1198 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
vg0208018838 NA 7.03E-11 mr1232 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
vg0208018838 NA 5.62E-10 mr1336 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
vg0208018838 NA 5.86E-06 mr1508 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
vg0208018838 NA 1.84E-22 mr1557 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
vg0208018838 NA 4.40E-13 mr1701 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
vg0208018838 NA 1.04E-11 mr1377_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