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Detailed information for vg0126639023:

Variant ID: vg0126639023 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 26639023
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GGTTATATTTTGAATTAGATTAAGTAATTTCATATAGTGATAGAGTGCATTATGTGTAACATACTGATCAAAGGGTTTTACTAAAGGAGTTATGGTCTAA[T/A]
TTTAGTGAAGGTGTAAAGTAGAATAAGTGGTATGCTAGCTATTTTCAGACTTAGCTAAGTGCTAGTTCGAGTTTAAATTTTTTTTGTGGTTGATTGTATC

Reverse complement sequence

GATACAATCAACCACAAAAAAAATTTAAACTCGAACTAGCACTTAGCTAAGTCTGAAAATAGCTAGCATACCACTTATTCTACTTTACACCTTCACTAAA[A/T]
TTAGACCATAACTCCTTTAGTAAAACCCTTTGATCAGTATGTTACACATAATGCACTCTATCACTATATGAAATTACTTAATCTAATTCAAAATATAACC

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 91.50% 8.40% 0.02% 0.00% NA
All Indica  2759 93.80% 6.20% 0.04% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 18.60% 81.40% 0.00% 0.00% NA
Indica I  595 98.20% 1.80% 0.00% 0.00% NA
Indica II  465 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 91.50% 8.50% 0.00% 0.00% NA
Indica Intermediate  786 89.70% 10.20% 0.13% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 92.70% 7.30% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 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
vg0126639023 T -> A LOC_Os01g46750.1 downstream_gene_variant ; 2074.0bp to feature; MODIFIER silent_mutation Average:62.257; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0126639023 T -> A LOC_Os01g46750.3 downstream_gene_variant ; 4695.0bp to feature; MODIFIER silent_mutation Average:62.257; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0126639023 T -> A LOC_Os01g46750.2 downstream_gene_variant ; 2074.0bp to feature; MODIFIER silent_mutation Average:62.257; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0126639023 T -> A LOC_Os01g46750.4 downstream_gene_variant ; 2074.0bp to feature; MODIFIER silent_mutation Average:62.257; most accessible tissue: Minghui63 panicle, score: 79.811 N N N N
vg0126639023 T -> A LOC_Os01g46750-LOC_Os01g46760 intergenic_region ; MODIFIER silent_mutation Average:62.257; most accessible tissue: Minghui63 panicle, score: 79.811 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)
vg0126639023 T A 0.0 -0.01 0.0 -0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0126639023 NA 7.13E-16 mr1166 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
vg0126639023 9.44E-06 9.42E-06 mr1366_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
vg0126639023 NA 1.21E-09 mr1388_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
vg0126639023 NA 8.89E-08 mr1469_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
vg0126639023 NA 4.15E-07 mr1511_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
vg0126639023 NA 1.10E-15 mr1583_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
vg0126639023 NA 1.87E-06 mr1743_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