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Detailed information for vg1121346183:

Variant ID: vg1121346183 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 21346183
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.94, T: 0.05, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


GTTGACGGTCGTTATCAATCAGTTTCGACCGTCAATATTACTAAAATAGAGGAGAACTAGTGATGCTTGCAATGCATATGTTTGTTAGAATAATAATATT[T/C]
CACTAGTATTAGGTATACTAACCTTTTATAGAGAATGACAATAAAGTGGAGGAGAATCGACATCAACTTAGACGATAAATCAATCGGACGATGTCGAGAA

Reverse complement sequence

TTCTCGACATCGTCCGATTGATTTATCGTCTAAGTTGATGTCGATTCTCCTCCACTTTATTGTCATTCTCTATAAAAGGTTAGTATACCTAATACTAGTG[A/G]
AATATTATTATTCTAACAAACATATGCATTGCAAGCATCACTAGTTCTCCTCTATTTTAGTAATATTGACGGTCGAAACTGATTGATAACGACCGTCAAC

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 60.00% 38.40% 0.36% 1.29% NA
All Indica  2759 86.60% 12.80% 0.11% 0.47% NA
All Japonica  1512 15.10% 84.10% 0.13% 0.66% NA
Aus  269 54.60% 27.50% 4.09% 13.75% NA
Indica I  595 78.00% 22.00% 0.00% 0.00% NA
Indica II  465 92.90% 4.70% 0.22% 2.15% NA
Indica III  913 88.40% 11.30% 0.11% 0.22% NA
Indica Intermediate  786 87.30% 12.50% 0.13% 0.13% NA
Temperate Japonica  767 10.80% 87.60% 0.26% 1.30% NA
Tropical Japonica  504 21.60% 78.40% 0.00% 0.00% NA
Japonica Intermediate  241 14.90% 85.10% 0.00% 0.00% NA
VI/Aromatic  96 27.10% 72.90% 0.00% 0.00% NA
Intermediate  90 50.00% 47.80% 1.11% 1.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1121346183 T -> DEL N N silent_mutation Average:58.411; most accessible tissue: Minghui63 young leaf, score: 81.195 N N N N
vg1121346183 T -> C LOC_Os11g36260.1 upstream_gene_variant ; 1178.0bp to feature; MODIFIER silent_mutation Average:58.411; most accessible tissue: Minghui63 young leaf, score: 81.195 N N N N
vg1121346183 T -> C LOC_Os11g36270.1 downstream_gene_variant ; 4547.0bp to feature; MODIFIER silent_mutation Average:58.411; most accessible tissue: Minghui63 young leaf, score: 81.195 N N N N
vg1121346183 T -> C LOC_Os11g36240-LOC_Os11g36260 intergenic_region ; MODIFIER silent_mutation Average:58.411; most accessible tissue: Minghui63 young leaf, score: 81.195 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)
vg1121346183 T C 0.0 0.0 0.0 0.0 0.0 0.0

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1121346183 NA 1.30E-06 mr1561_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
vg1121346183 NA 4.80E-07 mr1875_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
vg1121346183 1.51E-07 1.51E-07 mr1908_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