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Detailed information for vg1127591747:

Variant ID: vg1127591747 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 27591747
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:


TCTGGCTGTTCATTAGCTTGTTTGGTCAAATTGGGTGTTGAGAGTGATGAGCATTATGTAGTTTATTATGGAAAAGAGGGTTTGGCTGATCGACGAAAGC[A/G]
GGAAAGTAATGAGTCTTTTTGTTGGCCCTTTTTTTTAATTACTCTGAATGTTTTCCTGTCAAATAACCATCTGCACTCAGAATCAGAAAATTTTAACATA

Reverse complement sequence

TATGTTAAAATTTTCTGATTCTGAGTGCAGATGGTTATTTGACAGGAAAACATTCAGAGTAATTAAAAAAAAGGGCCAACAAAAAGACTCATTACTTTCC[T/C]
GCTTTCGTCGATCAGCCAAACCCTCTTTTCCATAATAAACTACATAATGCTCATCACTCTCAACACCCAATTTGACCAAACAAGCTAATGAACAGCCAGA

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 79.50% 20.30% 0.23% 0.00% NA
All Indica  2759 84.60% 15.20% 0.18% 0.00% NA
All Japonica  1512 72.90% 26.90% 0.20% 0.00% NA
Aus  269 53.20% 46.50% 0.37% 0.00% NA
Indica I  595 71.10% 28.90% 0.00% 0.00% NA
Indica II  465 93.80% 5.60% 0.65% 0.00% NA
Indica III  913 91.20% 8.70% 0.11% 0.00% NA
Indica Intermediate  786 81.70% 18.20% 0.13% 0.00% NA
Temperate Japonica  767 69.80% 29.90% 0.39% 0.00% NA
Tropical Japonica  504 85.10% 14.90% 0.00% 0.00% NA
Japonica Intermediate  241 57.70% 42.30% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 2.10% 1.04% 0.00% NA
Intermediate  90 91.10% 7.80% 1.11% 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
vg1127591747 A -> G LOC_Os11g45580.1 upstream_gene_variant ; 2561.0bp to feature; MODIFIER silent_mutation Average:72.088; most accessible tissue: Zhenshan97 flower, score: 98.806 N N N N
vg1127591747 A -> G LOC_Os11g45590.1 intron_variant ; MODIFIER silent_mutation Average:72.088; most accessible tissue: Zhenshan97 flower, score: 98.806 N N N N
vg1127591747 A -> G LOC_Os11g45590.2 intron_variant ; MODIFIER silent_mutation Average:72.088; most accessible tissue: Zhenshan97 flower, score: 98.806 N N N N
vg1127591747 A -> G LOC_Os11g45590.3 intron_variant ; MODIFIER silent_mutation Average:72.088; most accessible tissue: Zhenshan97 flower, score: 98.806 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)
vg1127591747 A G 0.01 0.01 0.0 0.0 0.01 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1127591747 NA 1.71E-06 mr1500 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
vg1127591747 NA 1.20E-06 mr1534 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
vg1127591747 4.86E-06 3.70E-06 mr1812 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