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Detailed information for vg1105795032:

Variant ID: vg1105795032 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 5795032
Reference Allele: AAlternative Allele: T,AAAT
Primary Allele: ASecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTGACTCGAGGTCGTCCTAGTCTTGGCGCCTATGCTACGCACAAAGCACAGCTAATAGAGCATAATCTTCAGCTTCTTAATTACTCACACTGTACAAAAA[A/T,AAAT]
AAATAAATAAAAAGAAATAAACCCCTGAAGTTTAATTCTTTTTGGACAGAGAAAATAGTTAGTTTGAATTGTAGGCGTACGTTTTGTCTGGACTTATTTG

Reverse complement sequence

CAAATAAGTCCAGACAAAACGTACGCCTACAATTCAAACTAACTATTTTCTCTGTCCAAAAAGAATTAAACTTCAGGGGTTTATTTCTTTTTATTTATTT[T/A,ATTT]
TTTTTGTACAGTGTGAGTAATTAAGAAGCTGAAGATTATGCTCTATTAGCTGTGCTTTGTGCGTAGCATAGGCGCCAAGACTAGGACGACCTCGAGTCAA

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 28.40% 9.60% 5.76% 56.03% AAAT: 0.19%
All Indica  2759 15.50% 0.60% 8.12% 75.79% NA
All Japonica  1512 58.50% 25.20% 2.25% 14.09% NA
Aus  269 2.20% 1.90% 2.97% 92.94% NA
Indica I  595 13.40% 0.50% 6.05% 80.00% NA
Indica II  465 11.40% 0.00% 13.98% 74.62% NA
Indica III  913 21.60% 0.10% 6.46% 71.85% NA
Indica Intermediate  786 12.30% 1.70% 8.14% 77.86% NA
Temperate Japonica  767 75.20% 14.00% 2.74% 8.08% NA
Tropical Japonica  504 45.40% 34.30% 0.79% 19.44% NA
Japonica Intermediate  241 32.40% 41.90% 3.73% 21.99% NA
VI/Aromatic  96 1.00% 40.60% 3.12% 46.88% AAAT: 8.33%
Intermediate  90 28.90% 12.20% 3.33% 54.44% AAAT: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg1105795032 A -> T LOC_Os11g10560.1 upstream_gene_variant ; 1249.0bp to feature; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> T LOC_Os11g10570.1 downstream_gene_variant ; 1975.0bp to feature; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> T LOC_Os11g10560-LOC_Os11g10570 intergenic_region ; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> DEL N N silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> AAAT LOC_Os11g10560.1 upstream_gene_variant ; 1250.0bp to feature; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> AAAT LOC_Os11g10570.1 downstream_gene_variant ; 1974.0bp to feature; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 N N N N
vg1105795032 A -> AAAT LOC_Os11g10560-LOC_Os11g10570 intergenic_region ; MODIFIER silent_mutation Average:45.502; most accessible tissue: Callus, score: 97.353 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)
vg1105795032 A AAAT -0.08 0.09 0.12 -0.03 -0.07 -0.12
vg1105795032 A T 0.01 -0.02 -0.02 -0.03 -0.04 -0.04

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1105795032 NA 9.00E-06 mr1205 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
vg1105795032 4.57E-06 4.57E-06 mr1372 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
vg1105795032 NA 2.92E-06 mr1991 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