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Detailed information for vg0103485561:

Variant ID: vg0103485561 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 3485561
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


TGTGTAGTACACCTCCGTCCCAAAATAAGTATAGCCATAGATATACGTGCTCAGCGTTTTGACCATCCGTCTTATTTAAAAAATTTATAAAAAAATATTT[A/T]
AAAAAATTAGTCACACATAGAGTGCCATTCATGTTTTATCATTTAATAACAATAAAATAAAAGTACTGATCATAATATTTTTTCAAATAAGACGAACGGT

Reverse complement sequence

ACCGTTCGTCTTATTTGAAAAAATATTATGATCAGTACTTTTATTTTATTGTTATTAAATGATAAAACATGAATGGCACTCTATGTGTGACTAATTTTTT[T/A]
AAATATTTTTTTATAAATTTTTTAAATAAGACGGATGGTCAAAACGCTGAGCACGTATATCTATGGCTATACTTATTTTGGGACGGAGGTGTACTACACA

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 76.20% 23.50% 0.32% 0.00% NA
All Indica  2759 65.30% 34.30% 0.43% 0.00% NA
All Japonica  1512 90.30% 9.70% 0.00% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 65.00% 34.80% 0.17% 0.00% NA
Indica II  465 66.70% 31.80% 1.51% 0.00% NA
Indica III  913 69.30% 30.60% 0.11% 0.00% NA
Indica Intermediate  786 59.90% 39.70% 0.38% 0.00% NA
Temperate Japonica  767 84.90% 15.10% 0.00% 0.00% NA
Tropical Japonica  504 96.40% 3.60% 0.00% 0.00% NA
Japonica Intermediate  241 95.00% 5.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 76.70% 20.00% 3.33% 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
vg0103485561 A -> T LOC_Os01g07370.1 upstream_gene_variant ; 982.0bp to feature; MODIFIER silent_mutation Average:88.643; most accessible tissue: Zhenshan97 root, score: 96.857 N N N N
vg0103485561 A -> T LOC_Os01g07370.2 upstream_gene_variant ; 3768.0bp to feature; MODIFIER silent_mutation Average:88.643; most accessible tissue: Zhenshan97 root, score: 96.857 N N N N
vg0103485561 A -> T LOC_Os01g07376.1 downstream_gene_variant ; 3749.0bp to feature; MODIFIER silent_mutation Average:88.643; most accessible tissue: Zhenshan97 root, score: 96.857 N N N N
vg0103485561 A -> T LOC_Os01g07370-LOC_Os01g07376 intergenic_region ; MODIFIER silent_mutation Average:88.643; most accessible tissue: Zhenshan97 root, score: 96.857 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)
vg0103485561 A T 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0103485561 NA 3.83E-06 mr1210 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
vg0103485561 NA 3.74E-06 mr1305 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
vg0103485561 1.87E-06 NA mr1380 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
vg0103485561 NA 9.29E-06 mr1380 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
vg0103485561 6.18E-06 NA mr1561 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
vg0103485561 3.55E-06 NA mr1937 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