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Detailed information for vg0802405704:

Variant ID: vg0802405704 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2405704
Reference Allele: TAlternative Allele: A
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTTCTCTTCTTTTTGCAAAATTGAATACTCCCTCTGTTAAAAAAAAAGATAAACCCTTGGTTTCCGTGTCATGTTTGACCATTCGTCTTATTTGAAAAAA[T/A]
TAAAAAGATAAGTCACGTATAAAGTATTAATCATGTTTTATCATCTAATAATAATGAAAATACTAATTATAAAAAAATTTAATATAAGACGAATAGTCAA

Reverse complement sequence

TTGACTATTCGTCTTATATTAAATTTTTTTATAATTAGTATTTTCATTATTATTAGATGATAAAACATGATTAATACTTTATACGTGACTTATCTTTTTA[A/T]
TTTTTTCAAATAAGACGAATGGTCAAACATGACACGGAAACCAAGGGTTTATCTTTTTTTTTAACAGAGGGAGTATTCAATTTTGCAAAAAGAAGAGAAA

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 93.50% 2.90% 1.14% 2.45% NA
All Indica  2759 95.00% 0.00% 1.01% 3.95% NA
All Japonica  1512 89.40% 8.80% 1.59% 0.26% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.60% 0.00% 1.34% 5.04% NA
Indica II  465 88.60% 0.00% 1.08% 10.32% NA
Indica III  913 99.20% 0.10% 0.44% 0.22% NA
Indica Intermediate  786 94.90% 0.00% 1.40% 3.69% NA
Temperate Japonica  767 97.80% 0.70% 1.17% 0.39% NA
Tropical Japonica  504 78.00% 20.00% 1.79% 0.20% NA
Japonica Intermediate  241 86.30% 11.20% 2.49% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 92.20% 2.20% 2.22% 3.33% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0802405704 T -> A LOC_Os08g04800.1 upstream_gene_variant ; 329.0bp to feature; MODIFIER silent_mutation Average:85.14; most accessible tissue: Callus, score: 96.454 N N N N
vg0802405704 T -> A LOC_Os08g04790-LOC_Os08g04800 intergenic_region ; MODIFIER silent_mutation Average:85.14; most accessible tissue: Callus, score: 96.454 N N N N
vg0802405704 T -> DEL N N silent_mutation Average:85.14; most accessible tissue: Callus, score: 96.454 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)
vg0802405704 T A -0.02 -0.03 -0.03 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802405704 4.61E-07 4.61E-07 mr1666 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