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Detailed information for vg1116342312:

Variant ID: vg1116342312 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 16342312
Reference Allele: CAlternative Allele: T
Primary Allele: TSecondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.85, T: 0.14, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:


CCACGTTTTTTATTTTTTTTATATTTTTGCTTCCAGTGCCACATCATCGCCACGTAGGACGAGGACCAAGTCAAACCGGCCACGTAGGTGCCATATCGGC[C/T]
AAAACCACCATTGAAACCGCTAAGGGATCTGCTTTGCACCGGTTTTGATAGTTGAGGGATCCGTATCTGGCTTTCTGGTTGAAGGATGAAAATCGGATAC

Reverse complement sequence

GTATCCGATTTTCATCCTTCAACCAGAAAGCCAGATACGGATCCCTCAACTATCAAAACCGGTGCAAAGCAGATCCCTTAGCGGTTTCAATGGTGGTTTT[G/A]
GCCGATATGGCACCTACGTGGCCGGTTTGACTTGGTCCTCGTCCTACGTGGCGATGATGTGGCACTGGAAGCAAAAATATAAAAAAAATAAAAAACGTGG

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 74.40% 24.40% 0.57% 0.57% NA
All Indica  2759 91.30% 7.00% 0.83% 0.87% NA
All Japonica  1512 43.60% 56.10% 0.20% 0.13% NA
Aus  269 97.00% 3.00% 0.00% 0.00% NA
Indica I  595 90.40% 8.60% 0.50% 0.50% NA
Indica II  465 95.10% 4.50% 0.22% 0.22% NA
Indica III  913 93.50% 6.10% 0.11% 0.22% NA
Indica Intermediate  786 87.30% 8.10% 2.29% 2.29% NA
Temperate Japonica  767 14.70% 85.00% 0.13% 0.13% NA
Tropical Japonica  504 72.60% 27.00% 0.20% 0.20% NA
Japonica Intermediate  241 74.70% 24.90% 0.41% 0.00% NA
VI/Aromatic  96 7.30% 92.70% 0.00% 0.00% NA
Intermediate  90 78.90% 18.90% 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
vg1116342312 C -> T LOC_Os11g28380.1 upstream_gene_variant ; 1730.0bp to feature; MODIFIER silent_mutation Average:82.714; most accessible tissue: Callus, score: 96.987 N N N N
vg1116342312 C -> T LOC_Os11g28400.1 upstream_gene_variant ; 1600.0bp to feature; MODIFIER silent_mutation Average:82.714; most accessible tissue: Callus, score: 96.987 N N N N
vg1116342312 C -> T LOC_Os11g28370.1 downstream_gene_variant ; 3773.0bp to feature; MODIFIER silent_mutation Average:82.714; most accessible tissue: Callus, score: 96.987 N N N N
vg1116342312 C -> T LOC_Os11g28390.1 intron_variant ; MODIFIER silent_mutation Average:82.714; most accessible tissue: Callus, score: 96.987 N N N N
vg1116342312 C -> DEL N N silent_mutation Average:82.714; most accessible tissue: Callus, score: 96.987 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)
vg1116342312 C T 0.06 0.08 0.06 0.06 0.06 0.06

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116342312 NA 1.34E-07 mr1229 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
vg1116342312 1.75E-06 NA mr1454 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
vg1116342312 NA 2.90E-07 mr1530 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
vg1116342312 NA 2.63E-08 mr1629 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