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Detailed information for vg1112896508:

Variant ID: vg1112896508 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 12896508
Reference Allele: TAlternative Allele: C
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:


GGAAAAGCTAAAAGAAATCCTCTTCCTCCTGTTGGGCTGTTTCCAGCCCATCTCTCCCTCTCTTGGCCCAGCCCAGCCGCCCCCTCTCCTTCCCTCTCTC[T/C]
CCTCCCCCTCCCTCTCCTTGGGCCGGCCCAGCTCATTCCCTCTCCCTCGGACTAAGTCCATCTTTCCTTCTCCGCGCGCCCCAGCCTGGGCAGGTGTGCT

Reverse complement sequence

AGCACACCTGCCCAGGCTGGGGCGCGCGGAGAAGGAAAGATGGACTTAGTCCGAGGGAGAGGGAATGAGCTGGGCCGGCCCAAGGAGAGGGAGGGGGAGG[A/G]
GAGAGAGGGAAGGAGAGGGGGCGGCTGGGCTGGGCCAAGAGAGGGAGAGATGGGCTGGAAACAGCCCAACAGGAGGAAGAGGATTTCTTTTAGCTTTTCC

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 41.20% 31.90% 1.10% 25.79% NA
All Indica  2759 14.00% 42.20% 1.67% 42.08% NA
All Japonica  1512 95.20% 1.70% 0.20% 2.91% NA
Aus  269 0.00% 100.00% 0.00% 0.00% NA
Indica I  595 37.10% 19.20% 1.34% 42.35% NA
Indica II  465 9.00% 63.40% 0.43% 27.10% NA
Indica III  913 2.20% 43.20% 1.53% 53.12% NA
Indica Intermediate  786 13.20% 46.10% 2.80% 37.91% NA
Temperate Japonica  767 96.90% 2.10% 0.00% 1.04% NA
Tropical Japonica  504 91.70% 1.40% 0.60% 6.35% NA
Japonica Intermediate  241 97.50% 0.80% 0.00% 1.66% NA
VI/Aromatic  96 85.40% 12.50% 2.08% 0.00% NA
Intermediate  90 42.20% 41.10% 1.11% 15.56% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1112896508 T -> DEL N N silent_mutation Average:59.172; most accessible tissue: Minghui63 young leaf, score: 87.677 N N N N
vg1112896508 T -> C LOC_Os11g22449.1 upstream_gene_variant ; 4319.0bp to feature; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 young leaf, score: 87.677 N N N N
vg1112896508 T -> C LOC_Os11g22440-LOC_Os11g22449 intergenic_region ; MODIFIER silent_mutation Average:59.172; most accessible tissue: Minghui63 young leaf, score: 87.677 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)
vg1112896508 T C -0.02 -0.01 -0.02 -0.02 -0.04 -0.03

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1112896508 NA 3.96E-23 mr1383 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
vg1112896508 NA 1.75E-87 mr1758 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
vg1112896508 NA 3.58E-07 mr1779 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
vg1112896508 NA 1.10E-06 mr1020_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
vg1112896508 NA 7.59E-08 mr1084_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
vg1112896508 NA 3.48E-22 mr1168_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
vg1112896508 NA 6.07E-09 mr1198_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
vg1112896508 NA 4.10E-07 mr1275_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
vg1112896508 NA 2.48E-15 mr1767_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
vg1112896508 NA 2.81E-18 mr1817_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
vg1112896508 1.46E-06 2.24E-07 mr1827_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
vg1112896508 NA 2.30E-09 mr1835_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