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Detailed information for vg1004671078:

Variant ID: vg1004671078 (JBrowse)Variation Type: SNP
Chromosome: chr10Position: 4671078
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.03, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:


ACTCAGAGAAAATGGCCGTTTGATTGGATCACAGGAAAAACGCAGGAATAAGATAAGAGAGATAGACTCAGAGAAAATGTTCCAAGAGGTTAGATCTCTT[G/A]
CTAACTTTCCTCCAAAATATACATAGGATTACCCATTCCATAAAAATTTTAAAGGATTAGATAGGATACAATCTTTTGTTTCAAAGACCTTCGTAGGATT

Reverse complement sequence

AATCCTACGAAGGTCTTTGAAACAAAAGATTGTATCCTATCTAATCCTTTAAAATTTTTATGGAATGGGTAATCCTATGTATATTTTGGAGGAAAGTTAG[C/T]
AAGAGATCTAACCTCTTGGAACATTTTCTCTGAGTCTATCTCTCTTATCTTATTCCTGCGTTTTTCCTGTGATCCAATCAAACGGCCATTTTCTCTGAGT

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 66.60% 20.50% 3.51% 9.31% NA
All Indica  2759 57.20% 25.10% 5.40% 12.36% NA
All Japonica  1512 78.00% 16.70% 0.73% 4.56% NA
Aus  269 98.90% 1.10% 0.00% 0.00% NA
Indica I  595 60.30% 21.20% 10.59% 7.90% NA
Indica II  465 65.60% 20.60% 3.66% 10.11% NA
Indica III  913 45.70% 31.90% 3.40% 19.06% NA
Indica Intermediate  786 63.10% 22.80% 4.83% 9.29% NA
Temperate Japonica  767 88.80% 8.70% 0.13% 2.35% NA
Tropical Japonica  504 69.20% 26.20% 0.79% 3.77% NA
Japonica Intermediate  241 62.20% 22.00% 2.49% 13.28% NA
VI/Aromatic  96 63.50% 10.40% 2.08% 23.96% NA
Intermediate  90 72.20% 15.60% 4.44% 7.78% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1004671078 G -> A LOC_Os10g08580.1 upstream_gene_variant ; 4087.0bp to feature; MODIFIER silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg1004671078 G -> A LOC_Os10g08590.1 upstream_gene_variant ; 1361.0bp to feature; MODIFIER silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg1004671078 G -> A LOC_Os10g08599.1 upstream_gene_variant ; 240.0bp to feature; MODIFIER silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg1004671078 G -> A LOC_Os10g08610.1 upstream_gene_variant ; 3872.0bp to feature; MODIFIER silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg1004671078 G -> A LOC_Os10g08590-LOC_Os10g08599 intergenic_region ; MODIFIER silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 N N N N
vg1004671078 G -> DEL N N silent_mutation Average:79.712; most accessible tissue: Minghui63 panicle, score: 92.38 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)
vg1004671078 G A 0.01 -0.01 -0.01 0.01 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1004671078 NA 4.29E-06 mr1038 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
vg1004671078 2.61E-07 1.26E-08 mr1327_2 Ind_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
vg1004671078 NA 5.27E-07 mr1800_2 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