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Detailed information for vg1102446151:

Variant ID: vg1102446151 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 2446151
Reference Allele: AAlternative Allele: T
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, T: 0.01, others allele: 0.00, population size: 84. )

Flanking Sequence (100 bp) in Reference Genome:


AAAGCGATAAATGAGTTTGGCTTGATAAATTATTTGAAGAGCTGGTTAAGTGTTTGAAGAGTCCGATTTAGAAATGTTGTTGGAGATGCTATTAGTTCTT[A/T]
AAAAAAAAACTACTGTTGCAAGAACTGCAGCTAGTAGGCACATCATCGCACGATGCATTGCAGGCGACGTCATCTGCTGCACTCGAGTGAACCCAAGTCT

Reverse complement sequence

AGACTTGGGTTCACTCGAGTGCAGCAGATGACGTCGCCTGCAATGCATCGTGCGATGATGTGCCTACTAGCTGCAGTTCTTGCAACAGTAGTTTTTTTTT[T/A]
AAGAACTAATAGCATCTCCAACAACATTTCTAAATCGGACTCTTCAAACACTTAACCAGCTCTTCAAATAATTTATCAAGCCAAACTCATTTATCGCTTT

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 83.40% 14.20% 2.05% 0.40% NA
All Indica  2759 77.60% 19.90% 2.14% 0.33% NA
All Japonica  1512 98.10% 1.40% 0.40% 0.07% NA
Aus  269 53.90% 33.10% 9.67% 3.35% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 70.80% 27.50% 1.72% 0.00% NA
Indica III  913 66.90% 30.40% 2.30% 0.33% NA
Indica Intermediate  786 77.70% 17.70% 3.82% 0.76% NA
Temperate Japonica  767 99.30% 0.70% 0.00% 0.00% NA
Tropical Japonica  504 96.40% 3.00% 0.40% 0.20% NA
Japonica Intermediate  241 97.90% 0.40% 1.66% 0.00% NA
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 82.20% 12.20% 5.56% 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
vg1102446151 A -> T LOC_Os11g05440.1 upstream_gene_variant ; 447.0bp to feature; MODIFIER silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg1102446151 A -> T LOC_Os11g05450.1 upstream_gene_variant ; 2040.0bp to feature; MODIFIER silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg1102446151 A -> T LOC_Os11g05430.1 downstream_gene_variant ; 2267.0bp to feature; MODIFIER silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg1102446151 A -> T LOC_Os11g05460.1 downstream_gene_variant ; 3756.0bp to feature; MODIFIER silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg1102446151 A -> T LOC_Os11g05440-LOC_Os11g05450 intergenic_region ; MODIFIER silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 N N N N
vg1102446151 A -> DEL N N silent_mutation Average:84.873; most accessible tissue: Zhenshan97 panicle, score: 93.02 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)
vg1102446151 A T -0.02 -0.01 -0.01 0.0 -0.02 -0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1102446151 1.92E-06 NA mr1606 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