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Detailed information for vg0308325055:

Variant ID: vg0308325055 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 8325055
Reference Allele: AAlternative Allele: G
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GAGTGGCAAAACAACACTGACATGCCACACGCAACAAGCGTGACAGTTTTGTACCGTCGTGACCAAATAACACTGCCACGCCATCTAGACCGGCATGACA[A/G]
TGTTGTTTTACCACGCCAGTCTGGCTGGCTTGGCTGAAAGGTTCATATCTTATAAATAAGTTTTGAAAGGGTTTATTTTTAAAATTAAAAAGTTCAAAAA

Reverse complement sequence

TTTTTGAACTTTTTAATTTTAAAAATAAACCCTTTCAAAACTTATTTATAAGATATGAACCTTTCAGCCAAGCCAGCCAGACTGGCGTGGTAAAACAACA[T/C]
TGTCATGCCGGTCTAGATGGCGTGGCAGTGTTATTTGGTCACGACGGTACAAAACTGTCACGCTTGTTGCGTGTGGCATGTCAGTGTTGTTTTGCCACTC

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 93.00% 7.00% 0.06% 0.00% NA
All Indica  2759 99.80% 0.20% 0.00% 0.00% NA
All Japonica  1512 78.90% 20.90% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.20% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
Temperate Japonica  767 60.40% 39.40% 0.26% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 94.20% 5.40% 0.41% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 91.10% 8.90% 0.00% 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
vg0308325055 A -> G LOC_Os03g15210.1 upstream_gene_variant ; 1369.0bp to feature; MODIFIER silent_mutation Average:61.275; most accessible tissue: Callus, score: 78.043 N N N N
vg0308325055 A -> G LOC_Os03g15200.1 downstream_gene_variant ; 3467.0bp to feature; MODIFIER silent_mutation Average:61.275; most accessible tissue: Callus, score: 78.043 N N N N
vg0308325055 A -> G LOC_Os03g15220.1 downstream_gene_variant ; 2229.0bp to feature; MODIFIER silent_mutation Average:61.275; most accessible tissue: Callus, score: 78.043 N N N N
vg0308325055 A -> G LOC_Os03g15230.1 downstream_gene_variant ; 4059.0bp to feature; MODIFIER silent_mutation Average:61.275; most accessible tissue: Callus, score: 78.043 N N N N
vg0308325055 A -> G LOC_Os03g15210-LOC_Os03g15220 intergenic_region ; MODIFIER silent_mutation Average:61.275; most accessible tissue: Callus, score: 78.043 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)
vg0308325055 A G 0.07 0.04 0.03 0.06 0.06 0.05

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0308325055 NA 3.37E-07 mr1026 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
vg0308325055 NA 1.24E-06 mr1171 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
vg0308325055 6.87E-07 NA mr1585 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
vg0308325055 NA 1.06E-07 mr1585 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
vg0308325055 NA 7.23E-16 mr1712 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
vg0308325055 NA 1.81E-06 mr1712 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
vg0308325055 8.46E-06 NA mr1779 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
vg0308325055 4.77E-06 4.77E-06 mr1779 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
vg0308325055 NA 5.66E-06 mr1910 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
vg0308325055 NA 1.37E-08 mr1946 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
vg0308325055 NA 4.54E-10 mr1977 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
vg0308325055 NA 3.32E-06 mr1977 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