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Detailed information for vg0105153133:

Variant ID: vg0105153133 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 5153133
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


ACGATAGATGGTGGCCCGTGGGCGGTATTGGTAAGGATATACTCCCTCCATCTCTACATGTCTGACGCCGTTGATTTTTTTTAAAATATATTTAACTATT[T/C]
GTCTTATTTAAAAACTTTTATGAAATATGTAAAACTATATGTATACATAAAAGTATATTTAACAATAAATCAAATGGTAGAAAAAGAATTGATAATTATT

Reverse complement sequence

AATAATTATCAATTCTTTTTCTACCATTTGATTTATTGTTAAATATACTTTTATGTATACATATAGTTTTACATATTTCATAAAAGTTTTTAAATAAGAC[A/G]
AATAGTTAAATATATTTTAAAAAAAATCAACGGCGTCAGACATGTAGAGATGGAGGGAGTATATCCTTACCAATACCGCCCACGGGCCACCATCTATCGT

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 67.60% 24.70% 0.78% 6.92% NA
All Indica  2759 99.10% 0.80% 0.04% 0.07% NA
All Japonica  1512 7.30% 70.20% 2.18% 20.30% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 98.50% 1.30% 0.00% 0.22% NA
Indica III  913 99.10% 0.80% 0.11% 0.00% NA
Indica Intermediate  786 98.70% 1.10% 0.00% 0.13% NA
Temperate Japonica  767 11.20% 72.20% 2.74% 13.82% NA
Tropical Japonica  504 3.80% 62.90% 1.79% 31.55% NA
Japonica Intermediate  241 2.50% 78.80% 1.24% 17.43% NA
VI/Aromatic  96 32.30% 51.00% 1.04% 15.62% NA
Intermediate  90 61.10% 33.30% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0105153133 T -> DEL N N silent_mutation Average:96.895; most accessible tissue: Minghui63 root, score: 99.467 N N N N
vg0105153133 T -> C LOC_Os01g09900.1 downstream_gene_variant ; 2485.0bp to feature; MODIFIER silent_mutation Average:96.895; most accessible tissue: Minghui63 root, score: 99.467 N N N N
vg0105153133 T -> C LOC_Os01g09900-LOC_Os01g09930 intergenic_region ; MODIFIER silent_mutation Average:96.895; most accessible tissue: Minghui63 root, score: 99.467 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)
vg0105153133 T C 0.01 0.02 0.01 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0105153133 1.27E-13 NA mr1057 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
vg0105153133 1.42E-06 9.83E-09 mr1057 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
vg0105153133 NA 2.13E-26 mr1238 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
vg0105153133 NA 3.80E-27 mr1309 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
vg0105153133 NA 4.94E-17 mr1484 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
vg0105153133 NA 9.50E-07 mr1677 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
vg0105153133 NA 7.03E-15 mr1900 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
vg0105153133 NA 5.32E-11 mr1945 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
vg0105153133 1.80E-14 NA mr1057_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
vg0105153133 2.39E-07 2.58E-08 mr1057_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
vg0105153133 NA 2.13E-32 mr1137_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
vg0105153133 1.82E-06 9.70E-32 mr1238_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
vg0105153133 4.17E-06 2.34E-28 mr1484_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
vg0105153133 NA 8.82E-28 mr1617_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
vg0105153133 NA 7.39E-10 mr1705_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
vg0105153133 NA 2.12E-32 mr1841_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
vg0105153133 NA 1.62E-22 mr1900_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
vg0105153133 1.32E-06 3.52E-23 mr1945_2 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