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Detailed information for vg1117402069:

Variant ID: vg1117402069 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17402069
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.01, others allele: 0.00, population size: 89. )

Flanking Sequence (100 bp) in Reference Genome:


ACGGCGTGAGAAAGGAGGACGGAAAAAAGTGACGGGAGTGGCATGGTTCCAATTTTAGAAATTTTCAGTGGCATGTAGCTGATATGACGAATAATAGTGG[C/T]
ATTTTTTTAATTTGACAAACTTATAAAGTTATAGTAGCATGGATCTAATTAACCCTTTAGGAGAGGTAGACAAGTTTATAGGCTAGTTGTTCAAGCACTT

Reverse complement sequence

AAGTGCTTGAACAACTAGCCTATAAACTTGTCTACCTCTCCTAAAGGGTTAATTAGATCCATGCTACTATAACTTTATAAGTTTGTCAAATTAAAAAAAT[G/A]
CCACTATTATTCGTCATATCAGCTACATGCCACTGAAAATTTCTAAAATTGGAACCATGCCACTCCCGTCACTTTTTTCCGTCCTCCTTTCTCACGCCGT

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 43.70% 27.10% 20.82% 8.34% NA
All Indica  2759 65.00% 13.50% 19.46% 1.99% NA
All Japonica  1512 13.20% 55.00% 19.58% 12.17% NA
Aus  269 7.10% 5.20% 32.34% 55.39% NA
Indica I  595 77.60% 16.00% 5.88% 0.50% NA
Indica II  465 43.70% 14.20% 36.34% 5.81% NA
Indica III  913 70.20% 10.30% 18.95% 0.55% NA
Indica Intermediate  786 62.10% 15.00% 20.36% 2.54% NA
Temperate Japonica  767 1.70% 79.70% 8.74% 9.91% NA
Tropical Japonica  504 33.10% 22.20% 34.72% 9.92% NA
Japonica Intermediate  241 8.30% 45.20% 22.41% 24.07% NA
VI/Aromatic  96 22.90% 36.50% 38.54% 2.08% NA
Intermediate  90 33.30% 32.20% 30.00% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1117402069 C -> T LOC_Os11g29945.1 upstream_gene_variant ; 1338.0bp to feature; MODIFIER silent_mutation Average:79.306; most accessible tissue: Zhenshan97 panicle, score: 93.244 N N N N
vg1117402069 C -> T LOC_Os11g29940.1 downstream_gene_variant ; 114.0bp to feature; MODIFIER silent_mutation Average:79.306; most accessible tissue: Zhenshan97 panicle, score: 93.244 N N N N
vg1117402069 C -> T LOC_Os11g29950.1 downstream_gene_variant ; 3389.0bp to feature; MODIFIER silent_mutation Average:79.306; most accessible tissue: Zhenshan97 panicle, score: 93.244 N N N N
vg1117402069 C -> T LOC_Os11g29940-LOC_Os11g29945 intergenic_region ; MODIFIER silent_mutation Average:79.306; most accessible tissue: Zhenshan97 panicle, score: 93.244 N N N N
vg1117402069 C -> DEL N N silent_mutation Average:79.306; most accessible tissue: Zhenshan97 panicle, score: 93.244 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)
vg1117402069 C T 0.0 -0.01 -0.01 0.0 0.0 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117402069 NA 7.00E-06 mr1159_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
vg1117402069 3.35E-06 NA mr1659_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
vg1117402069 NA 1.50E-09 mr1739_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
vg1117402069 NA 2.40E-06 mr1759_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