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Detailed information for vg0611482704:

Variant ID: vg0611482704 (JBrowse)Variation Type: SNP
Chromosome: chr06Position: 11482704
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.85, T: 0.15, others allele: 0.00, population size: 93. )

Flanking Sequence (100 bp) in Reference Genome:


TGATCATTCAGAGAAGACAACACTACACATCCCAACTCCAAAAATCTTCCAGGCGACGCCAATTTGACATCCATCGAAACAAAGAAACAGAATATTTTTT[A/T]
AAAAAATAACTGGAAAGACGCTGCGAGAGACTCACCCATACACCGAACCGAAGAGCATAGCGAGCAGCGGCGGCCGGCGGCCGGCCTCGCTCACCACCAT

Reverse complement sequence

ATGGTGGTGAGCGAGGCCGGCCGCCGGCCGCCGCTGCTCGCTATGCTCTTCGGTTCGGTGTATGGGTGAGTCTCTCGCAGCGTCTTTCCAGTTATTTTTT[T/A]
AAAAAATATTCTGTTTCTTTGTTTCGATGGATGTCAAATTGGCGTCGCCTGGAAGATTTTTGGAGTTGGGATGTGTAGTGTTGTCTTCTCTGAATGATCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.80% 28.60% 0.11% 1.52% NA
All Indica  2759 57.50% 39.70% 0.18% 2.57% NA
All Japonica  1512 90.00% 9.90% 0.00% 0.07% NA
Aus  269 74.00% 26.00% 0.00% 0.00% NA
Indica I  595 74.30% 25.70% 0.00% 0.00% NA
Indica II  465 78.50% 21.10% 0.00% 0.43% NA
Indica III  913 36.60% 56.70% 0.22% 6.46% NA
Indica Intermediate  786 56.70% 41.60% 0.38% 1.27% NA
Temperate Japonica  767 96.90% 3.10% 0.00% 0.00% NA
Tropical Japonica  504 76.20% 23.60% 0.00% 0.20% NA
Japonica Intermediate  241 97.10% 2.90% 0.00% 0.00% NA
VI/Aromatic  96 91.70% 8.30% 0.00% 0.00% NA
Intermediate  90 70.00% 30.00% 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
vg0611482704 A -> T LOC_Os06g20030.1 upstream_gene_variant ; 404.0bp to feature; MODIFIER silent_mutation Average:93.953; most accessible tissue: Callus, score: 96.149 N N N N
vg0611482704 A -> T LOC_Os06g20020.1 downstream_gene_variant ; 4902.0bp to feature; MODIFIER silent_mutation Average:93.953; most accessible tissue: Callus, score: 96.149 N N N N
vg0611482704 A -> T LOC_Os06g20040.1 downstream_gene_variant ; 4252.0bp to feature; MODIFIER silent_mutation Average:93.953; most accessible tissue: Callus, score: 96.149 N N N N
vg0611482704 A -> T LOC_Os06g20020-LOC_Os06g20030 intergenic_region ; MODIFIER silent_mutation Average:93.953; most accessible tissue: Callus, score: 96.149 N N N N
vg0611482704 A -> DEL N N silent_mutation Average:93.953; most accessible tissue: Callus, score: 96.149 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)
vg0611482704 A T 0.01 0.01 0.01 0.0 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0611482704 7.27E-07 NA mr1020 Jap_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
vg0611482704 NA 4.96E-07 mr1218 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
vg0611482704 5.03E-08 5.03E-08 mr1478 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
vg0611482704 4.71E-08 1.90E-08 mr1971 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
vg0611482704 3.90E-07 1.62E-08 mr1165_2 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
vg0611482704 8.26E-06 8.22E-06 mr1197_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
vg0611482704 NA 1.90E-09 mr1221_2 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
vg0611482704 5.99E-06 6.00E-06 mr1477_2 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
vg0611482704 NA 2.97E-10 mr1850_2 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