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Detailed information for vg1108600324:

Variant ID: vg1108600324 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 8600324
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.09, C: 0.01, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:


TATACATATAATTTTACATATTTCACAAAAGTTTTTGAATAAGACAAACGGCTAAATATGTGCTAAAAAGTCAACGGTGTCAAATATTTAGAAAACGGAG[G/A]
GAGTATATGACACCAGTTTGCTGCCAAACTAGCTACCCGCGCCGGCGCCGTGCCTCGAATCAAACCTCACGATCGATCGAATCATGGCGCTACGTACAGT

Reverse complement sequence

ACTGTACGTAGCGCCATGATTCGATCGATCGTGAGGTTTGATTCGAGGCACGGCGCCGGCGCGGGTAGCTAGTTTGGCAGCAAACTGGTGTCATATACTC[C/T]
CTCCGTTTTCTAAATATTTGACACCGTTGACTTTTTAGCACATATTTAGCCGTTTGTCTTATTCAAAAACTTTTGTGAAATATGTAAAATTATATGTATA

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 75.90% 23.90% 0.23% 0.00% NA
All Indica  2759 63.00% 36.60% 0.40% 0.00% NA
All Japonica  1512 93.30% 6.70% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 34.50% 65.20% 0.34% 0.00% NA
Indica II  465 86.50% 13.10% 0.43% 0.00% NA
Indica III  913 64.00% 35.70% 0.33% 0.00% NA
Indica Intermediate  786 69.50% 30.00% 0.51% 0.00% NA
Temperate Japonica  767 98.20% 1.80% 0.00% 0.00% NA
Tropical Japonica  504 85.10% 14.90% 0.00% 0.00% NA
Japonica Intermediate  241 94.60% 5.40% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg1108600324 G -> A LOC_Os11g15230.1 upstream_gene_variant ; 1351.0bp to feature; MODIFIER silent_mutation Average:68.528; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg1108600324 G -> A LOC_Os11g15240.1 upstream_gene_variant ; 2553.0bp to feature; MODIFIER silent_mutation Average:68.528; most accessible tissue: Zhenshan97 root, score: 88.238 N N N N
vg1108600324 G -> A LOC_Os11g15230-LOC_Os11g15240 intergenic_region ; MODIFIER silent_mutation Average:68.528; most accessible tissue: Zhenshan97 root, score: 88.238 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)
vg1108600324 G A -0.04 -0.06 -0.03 -0.01 -0.07 -0.09

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1108600324 NA 3.19E-06 mr1693 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
vg1108600324 NA 3.68E-06 mr1123_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
vg1108600324 NA 5.53E-10 mr1134_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
vg1108600324 NA 7.72E-11 mr1504_2 Jap_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
vg1108600324 NA 5.79E-08 mr1672_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