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Detailed information for vg1124950335:

Variant ID: vg1124950335 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 24950335
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 117. )

Flanking Sequence (100 bp) in Reference Genome:


ATGTAATCCTAAATTCCATATTTGATTAATTGGGTTCCCTTTGTCTCGCTACTACCTCTGTTGCAAAATACAATAACTTCTACTTATATATTTACACAAA[C/T]
ATTTATCCAAATACATAATTAAAAGTTGCTATATTTTGTAACGGACGAAACAAATCCAAATTCTTTGCATCATATTCTGAAGTCTGAAACTCTGAACCTT

Reverse complement sequence

AAGGTTCAGAGTTTCAGACTTCAGAATATGATGCAAAGAATTTGGATTTGTTTCGTCCGTTACAAAATATAGCAACTTTTAATTATGTATTTGGATAAAT[G/A]
TTTGTGTAAATATATAAGTAGAAGTTATTGTATTTTGCAACAGAGGTAGTAGCGAGACAAAGGGAACCCAATTAATCAAATATGGAATTTAGGATTACAT

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 84.70% 15.20% 0.08% 0.00% NA
All Indica  2759 82.90% 17.10% 0.07% 0.00% NA
All Japonica  1512 89.20% 10.70% 0.13% 0.00% NA
Aus  269 72.50% 27.50% 0.00% 0.00% NA
Indica I  595 95.80% 4.20% 0.00% 0.00% NA
Indica II  465 86.70% 13.30% 0.00% 0.00% NA
Indica III  913 73.60% 26.30% 0.11% 0.00% NA
Indica Intermediate  786 81.60% 18.30% 0.13% 0.00% NA
Temperate Japonica  767 98.30% 1.70% 0.00% 0.00% NA
Tropical Japonica  504 81.30% 18.50% 0.20% 0.00% NA
Japonica Intermediate  241 76.30% 23.20% 0.41% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 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
vg1124950335 C -> T LOC_Os11g41590.1 downstream_gene_variant ; 661.0bp to feature; MODIFIER silent_mutation Average:78.917; most accessible tissue: Minghui63 young leaf, score: 96.8 N N N N
vg1124950335 C -> T LOC_Os11g41600.1 downstream_gene_variant ; 446.0bp to feature; MODIFIER silent_mutation Average:78.917; most accessible tissue: Minghui63 young leaf, score: 96.8 N N N N
vg1124950335 C -> T LOC_Os11g41600.2 downstream_gene_variant ; 446.0bp to feature; MODIFIER silent_mutation Average:78.917; most accessible tissue: Minghui63 young leaf, score: 96.8 N N N N
vg1124950335 C -> T LOC_Os11g41590-LOC_Os11g41600 intergenic_region ; MODIFIER silent_mutation Average:78.917; most accessible tissue: Minghui63 young leaf, score: 96.8 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)
vg1124950335 C T 0.01 0.0 -0.01 0.01 0.01 0.01

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1124950335 4.05E-09 3.13E-09 mr1238 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
vg1124950335 1.13E-08 2.03E-08 mr1309 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
vg1124950335 6.04E-06 1.77E-06 mr1841 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
vg1124950335 8.53E-06 NA mr1238_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
vg1124950335 6.01E-06 NA mr1484_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
vg1124950335 1.80E-07 1.27E-06 mr1841_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