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Detailed information for vg0110522578:

Variant ID: vg0110522578 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 10522578
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.84, C: 0.16, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:


TTACATCCGAATTACAACAGTTCAAACATGGTAGTAGTACAATTAAGGCGGCGCCCATTTTTTAAGAATTTTAGATTTCGAGAAGCGACCAGTAAGAATA[T/C]
GAGGAAACTGAGAAAACTCAGTTTTTGATTTTTAATTAGTGACATGTTTACTTTGATGCCAAAAAAAACATTACCAAATTTTGGCATTGTCGAAATTTTG

Reverse complement sequence

CAAAATTTCGACAATGCCAAAATTTGGTAATGTTTTTTTTGGCATCAAAGTAAACATGTCACTAATTAAAAATCAAAAACTGAGTTTTCTCAGTTTCCTC[A/G]
TATTCTTACTGGTCGCTTCTCGAAATCTAAAATTCTTAAAAAATGGGCGCCGCCTTAATTGTACTACTACCATGTTTGAACTGTTGTAATTCGGATGTAA

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.70% 8.10% 0.17% 0.00% NA
All Indica  2759 86.20% 13.50% 0.29% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 74.80% 25.00% 0.17% 0.00% NA
Indica II  465 90.30% 9.20% 0.43% 0.00% NA
Indica III  913 91.60% 8.40% 0.00% 0.00% NA
Indica Intermediate  786 86.10% 13.20% 0.64% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 97.90% 2.10% 0.00% 0.00% NA
Intermediate  90 93.30% 6.70% 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
vg0110522578 T -> C LOC_Os01g18670.1 upstream_gene_variant ; 1296.0bp to feature; MODIFIER silent_mutation Average:79.464; most accessible tissue: Minghui63 root, score: 93.154 N N N N
vg0110522578 T -> C LOC_Os01g18670-LOC_Os01g18680 intergenic_region ; MODIFIER silent_mutation Average:79.464; most accessible tissue: Minghui63 root, score: 93.154 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)
vg0110522578 T C -0.01 0.0 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0110522578 NA 1.17E-06 mr1037 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
vg0110522578 4.00E-06 3.98E-06 mr1452 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
vg0110522578 NA 4.41E-06 mr1513 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
vg0110522578 NA 8.84E-07 mr1590 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
vg0110522578 NA 2.16E-06 mr1964 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
vg0110522578 NA 6.92E-06 mr1981 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