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Detailed information for vg0824951704:

Variant ID: vg0824951704 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 24951704
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.76, C: 0.24, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TGATGATACCCCTATAGTATGTATAACTATGTATTCTCTTCGTTCCAAAATACATTACGAGTCGTGGTTGATTTATTTTATGATAAAAGAAAACTATGTG[T/C]
GAGAAAAAGAAAAAAAAAGGGTGATATCCATTGACCTTGACGCAGCATCATACTAGTATCCTGCAGCGGATGTTAATTCACCACGTGAATTCGTGGTCGC

Reverse complement sequence

GCGACCACGAATTCACGTGGTGAATTAACATCCGCTGCAGGATACTAGTATGATGCTGCGTCAAGGTCAATGGATATCACCCTTTTTTTTTCTTTTTCTC[A/G]
CACATAGTTTTCTTTTATCATAAAATAAATCAACCACGACTCGTAATGTATTTTGGAACGAAGAGAATACATAGTTATACATACTATAGGGGTATCATCA

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 72.40% 27.20% 0.17% 0.28% NA
All Indica  2759 62.50% 36.90% 0.22% 0.40% NA
All Japonica  1512 99.80% 0.10% 0.07% 0.00% NA
Aus  269 10.00% 89.60% 0.00% 0.37% NA
Indica I  595 64.70% 34.30% 0.34% 0.67% NA
Indica II  465 75.10% 24.70% 0.00% 0.22% NA
Indica III  913 46.30% 53.50% 0.11% 0.11% NA
Indica Intermediate  786 72.30% 26.70% 0.38% 0.64% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.20% 0.40% 0.41% 0.00% NA
VI/Aromatic  96 93.80% 6.20% 0.00% 0.00% NA
Intermediate  90 77.80% 20.00% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0824951704 T -> C LOC_Os08g39450.1 upstream_gene_variant ; 2228.0bp to feature; MODIFIER silent_mutation Average:99.643; most accessible tissue: Minghui63 young leaf, score: 99.919 N N N N
vg0824951704 T -> C LOC_Os08g39440.1 downstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:99.643; most accessible tissue: Minghui63 young leaf, score: 99.919 N N N N
vg0824951704 T -> C LOC_Os08g39440.2 downstream_gene_variant ; 4653.0bp to feature; MODIFIER silent_mutation Average:99.643; most accessible tissue: Minghui63 young leaf, score: 99.919 N N N N
vg0824951704 T -> C LOC_Os08g39440-LOC_Os08g39450 intergenic_region ; MODIFIER silent_mutation Average:99.643; most accessible tissue: Minghui63 young leaf, score: 99.919 N N N N
vg0824951704 T -> DEL N N silent_mutation Average:99.643; most accessible tissue: Minghui63 young leaf, score: 99.919 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)
vg0824951704 T C 0.0 -0.01 0.0 -0.02 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0824951704 2.78E-07 4.21E-26 mr1874 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
vg0824951704 1.39E-06 1.45E-11 mr1874 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
vg0824951704 NA 7.41E-16 mr1587_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
vg0824951704 1.73E-09 5.25E-37 mr1874_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
vg0824951704 1.19E-08 1.67E-14 mr1874_2 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