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Detailed information for vg0527971405:

Variant ID: vg0527971405 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 27971405
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 128. )

Flanking Sequence (100 bp) in Reference Genome:


GGTAGCCATGGCACATCGGGACGACCGGACGAGTATACGTCCATTCTTCTCTCAGTACTCCCTAGTCCCTAGTCTTAAAAAAAAAAACTCAATTCCTAAC[G/A]
TTAGTTCCAATTTTTTTTTCCAAACTTCTAACTTTTTCATCACATCAAAACTTTCCTACGCACACAAACTTCCAACTTTTTTATCACATCATCGTAATTT

Reverse complement sequence

AAATTACGATGATGTGATAAAAAAGTTGGAAGTTTGTGTGCGTAGGAAAGTTTTGATGTGATGAAAAAGTTAGAAGTTTGGAAAAAAAAATTGGAACTAA[C/T]
GTTAGGAATTGAGTTTTTTTTTTTAAGACTAGGGACTAGGGAGTACTGAGAGAAGAATGGACGTATACTCGTCCGGTCGTCCCGATGTGCCATGGCTACC

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 84.00% 14.50% 1.50% 0.00% NA
All Indica  2759 94.60% 5.30% 0.07% 0.00% NA
All Japonica  1512 65.10% 30.50% 4.37% 0.00% NA
Aus  269 99.30% 0.70% 0.00% 0.00% NA
Indica I  595 99.20% 0.80% 0.00% 0.00% NA
Indica II  465 78.50% 21.10% 0.43% 0.00% NA
Indica III  913 99.80% 0.20% 0.00% 0.00% NA
Indica Intermediate  786 94.80% 5.20% 0.00% 0.00% NA
Temperate Japonica  767 57.10% 36.10% 6.78% 0.00% NA
Tropical Japonica  504 86.90% 13.10% 0.00% 0.00% NA
Japonica Intermediate  241 45.20% 49.00% 5.81% 0.00% NA
VI/Aromatic  96 27.10% 71.90% 1.04% 0.00% NA
Intermediate  90 91.10% 6.70% 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
vg0527971405 G -> A LOC_Os05g48800.1 upstream_gene_variant ; 317.0bp to feature; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 N N N N
vg0527971405 G -> A LOC_Os05g48800.2 upstream_gene_variant ; 317.0bp to feature; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 N N N N
vg0527971405 G -> A LOC_Os05g48800.3 upstream_gene_variant ; 317.0bp to feature; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 N N N N
vg0527971405 G -> A LOC_Os05g48810.1 downstream_gene_variant ; 886.0bp to feature; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 N N N N
vg0527971405 G -> A LOC_Os05g48820.1 downstream_gene_variant ; 4251.0bp to feature; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 N N N N
vg0527971405 G -> A LOC_Os05g48800-LOC_Os05g48810 intergenic_region ; MODIFIER silent_mutation Average:98.201; most accessible tissue: Minghui63 root, score: 98.961 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)
vg0527971405 G A -0.02 -0.01 -0.01 0.0 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0527971405 1.68E-06 NA mr1092 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
vg0527971405 NA 2.17E-06 mr1092 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