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Detailed information for vg0906399143:

Variant ID: vg0906399143 (JBrowse)Variation Type: SNP
Chromosome: chr09Position: 6399143
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.04, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


CTCAAAAAAAGAAAAAGATAAAGTGAGGTAGTACAAAGCTTATTGCAATGTAAGAGCAAGTTGAATAGTATAGCCATCCTCCAATTCATGTATAATCAAT[T/C]
TAATAGCTCATTCATATAATAGTTACATACTATACTATTAATATCTAGTCCCACCTATCATAGACACACTTCGTCTTAGAGTTCGTGCTACAGCTGGCTA

Reverse complement sequence

TAGCCAGCTGTAGCACGAACTCTAAGACGAAGTGTGTCTATGATAGGTGGGACTAGATATTAATAGTATAGTATGTAACTATTATATGAATGAGCTATTA[A/G]
ATTGATTATACATGAATTGGAGGATGGCTATACTATTCAACTTGCTCTTACATTGCAATAAGCTTTGTACTACCTCACTTTATCTTTTTCTTTTTTTGAG

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 58.40% 31.20% 3.24% 7.19% NA
All Indica  2759 81.40% 6.50% 3.84% 8.26% NA
All Japonica  1512 15.20% 81.90% 2.78% 0.13% NA
Aus  269 58.40% 2.20% 0.37% 39.03% NA
Indica I  595 89.20% 3.90% 3.70% 3.19% NA
Indica II  465 80.20% 7.50% 4.30% 7.96% NA
Indica III  913 78.50% 6.90% 3.40% 11.17% NA
Indica Intermediate  786 79.50% 7.40% 4.20% 8.91% NA
Temperate Japonica  767 5.70% 93.10% 1.04% 0.13% NA
Tropical Japonica  504 14.90% 83.30% 1.79% 0.00% NA
Japonica Intermediate  241 46.10% 43.20% 10.37% 0.41% NA
VI/Aromatic  96 85.40% 12.50% 1.04% 1.04% NA
Intermediate  90 50.00% 42.20% 3.33% 4.44% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0906399143 T -> DEL N N silent_mutation Average:99.118; most accessible tissue: Zhenshan97 young leaf, score: 99.892 N N N N
vg0906399143 T -> C LOC_Os09g11470-LOC_Os09g11480 intergenic_region ; MODIFIER silent_mutation Average:99.118; most accessible tissue: Zhenshan97 young leaf, score: 99.892 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)
vg0906399143 T C -0.01 -0.01 -0.02 -0.03 -0.01 -0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0906399143 NA 1.75E-06 mr1113_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
vg0906399143 NA 4.95E-06 mr1240_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
vg0906399143 NA 2.78E-06 mr1496_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
vg0906399143 2.33E-06 NA mr1954_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