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Detailed information for vg1117639792:

Variant ID: vg1117639792 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 17639792
Reference Allele: GAlternative Allele: A
Primary Allele: ASecondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:


ACTGTCATGAAACTCCAGAATAGTTTACTACGCTAAACACAGCAAAGAAACTGAGAATCAGGGAGGAGAGAGTATAACACAACCAAAGGTAACAGCTTTC[G/A]
GTTTTGCATGCCCACGCTCTAGCGAGTAACCCATGAAATAACCCGAACGCTAACGGGAGTACCCACTGAACAACACTACTATACAATACTAGACCTTAAC

Reverse complement sequence

GTTAAGGTCTAGTATTGTATAGTAGTGTTGTTCAGTGGGTACTCCCGTTAGCGTTCGGGTTATTTCATGGGTTACTCGCTAGAGCGTGGGCATGCAAAAC[C/T]
GAAAGCTGTTACCTTTGGTTGTGTTATACTCTCTCCTCCCTGATTCTCAGTTTCTTTGCTGTGTTTAGCGTAGTAAACTATTCTGGAGTTTCATGACAGT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.60% 30.10% 0.32% 0.00% NA
All Indica  2759 89.60% 10.10% 0.29% 0.00% NA
All Japonica  1512 29.60% 70.00% 0.33% 0.00% NA
Aus  269 94.10% 5.90% 0.00% 0.00% NA
Indica I  595 76.50% 23.00% 0.50% 0.00% NA
Indica II  465 98.30% 1.50% 0.22% 0.00% NA
Indica III  913 92.10% 7.70% 0.22% 0.00% NA
Indica Intermediate  786 91.60% 8.10% 0.25% 0.00% NA
Temperate Japonica  767 32.90% 67.10% 0.00% 0.00% NA
Tropical Japonica  504 33.90% 65.10% 0.99% 0.00% NA
Japonica Intermediate  241 10.40% 89.60% 0.00% 0.00% NA
VI/Aromatic  96 52.10% 47.90% 0.00% 0.00% NA
Intermediate  90 73.30% 24.40% 2.22% 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
vg1117639792 G -> A LOC_Os11g30370.1 intron_variant ; MODIFIER silent_mutation Average:70.813; most accessible tissue: Zhenshan97 root, score: 89.27 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)
vg1117639792 G A -0.03 -0.02 -0.02 0.0 -0.01 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1117639792 NA 1.94E-06 mr1445 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
vg1117639792 NA 1.25E-13 mr1449 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
vg1117639792 NA 1.79E-06 mr1527 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
vg1117639792 NA 6.47E-06 mr1902 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
vg1117639792 NA 5.24E-07 mr1354_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
vg1117639792 NA 2.02E-06 mr1902_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