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Detailed information for vg1123942722:

Variant ID: vg1123942722 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 23942722
Reference Allele: AGAGAGAGAlternative Allele: GGAGAGAG,TGAGAGAG,A,AGGAGAGAG
Primary Allele: AGAGAGAGSecondary Allele: GGAGAGAG

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


CGTGTTGGCCCGTGAAGGCCCAAATAGGATCCAATAAGAGAGGAGGGCCTCCTGGATTCCGCGTTGCCGCCTTCAATTCCATTCGAACGAAACGAGGAGA[AGAGAGAG/GGAGAGAG,TGAGAGAG,A,AGGAGAGAG]
GAGAGAGGAGAGAGAGGGGTTTGTGTGGCTGCGAGTGGGCCCCATGTCGACGTCGGCGGCGGCGTCGGCGGCGGCGGAGCAGCAGCAGGAGGAGGGGGAG

Reverse complement sequence

CTCCCCCTCCTCCTGCTGCTGCTCCGCCGCCGCCGACGCCGCCGCCGACGTCGACATGGGGCCCACTCGCAGCCACACAAACCCCTCTCTCTCCTCTCTC[CTCTCTCT/CTCTCTCC,CTCTCTCA,T,CTCTCTCCT]
TCTCCTCGTTTCGTTCGAATGGAATTGAAGGCGGCAACGCGGAATCCAGGAGGCCCTCCTCTCTTATTGGATCCTATTTGGGCCTTCACGGGCCAACACG

Allele Frequencies:

Populations Population SizeFrequency of AGAGAGAG(primary allele) Frequency of GGAGAGAG(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 49.80% 37.70% 6.24% 1.93% TGAGAGAG: 3.98%; A: 0.34%; AGGAGAGAG: 0.04%
All Indica  2759 50.60% 35.80% 3.81% 3.30% TGAGAGAG: 6.45%; A: 0.04%
All Japonica  1512 50.60% 38.60% 10.32% 0.00% TGAGAGAG: 0.46%
Aus  269 43.10% 55.80% 1.12% 0.00% NA
Indica I  595 71.40% 25.90% 1.34% 0.00% TGAGAGAG: 1.34%
Indica II  465 47.10% 42.20% 7.10% 1.29% TGAGAGAG: 2.37%
Indica III  913 41.10% 37.80% 2.08% 8.76% TGAGAGAG: 10.19%; A: 0.11%
Indica Intermediate  786 48.00% 37.30% 5.73% 0.64% TGAGAGAG: 8.40%
Temperate Japonica  767 50.10% 37.50% 12.39% 0.00% NA
Tropical Japonica  504 52.60% 38.50% 8.73% 0.00% TGAGAGAG: 0.20%
Japonica Intermediate  241 48.10% 42.30% 7.05% 0.00% TGAGAGAG: 2.49%
VI/Aromatic  96 37.50% 26.00% 19.79% 0.00% A: 14.58%; AGGAGAGAG: 2.08%
Intermediate  90 45.60% 36.70% 13.33% 0.00% TGAGAGAG: 3.33%; A: 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
vg1123942722 AGAGAGAG -> TGAGAGAG LOC_Os11g40150.1 5_prime_UTR_premature_start_codon_gain_variant ; LOW silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> TGAGAGAG LOC_Os11g40150.1 5_prime_UTR_variant ; 51.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> TGAGAGAG LOC_Os11g40140.1 upstream_gene_variant ; 178.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> TGAGAGAG LOC_Os11g40160.1 upstream_gene_variant ; 4318.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> A LOC_Os11g40150.1 5_prime_UTR_variant ; 30.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> A LOC_Os11g40140.1 upstream_gene_variant ; 179.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> A LOC_Os11g40160.1 upstream_gene_variant ; 4317.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> AGGAGAGAG LOC_Os11g40150.1 5_prime_UTR_variant ; 49.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> AGGAGAGAG LOC_Os11g40140.1 upstream_gene_variant ; 180.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> AGGAGAGAG LOC_Os11g40160.1 upstream_gene_variant ; 4316.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> DEL N N silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> GGAGAGAG LOC_Os11g40150.1 5_prime_UTR_variant ; 51.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> GGAGAGAG LOC_Os11g40140.1 upstream_gene_variant ; 178.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 N N N N
vg1123942722 AGAGAGAG -> GGAGAGAG LOC_Os11g40160.1 upstream_gene_variant ; 4318.0bp to feature; MODIFIER silent_mutation Average:99.411; most accessible tissue: Zhenshan97 panicle, score: 99.859 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)
vg1123942722 AGAGA* A -0.02 -0.03 -0.01 0.0 0.01 0.01
vg1123942722 AGAGA* AGGAG* 0.09 0.11 0.1 0.04 0.06 0.07
vg1123942722 AGAGA* GGAGA* 0.03 0.03 0.02 0.02 0.02 0.02
vg1123942722 AGAGA* TGAGA* 0.02 0.03 0.02 0.02 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1123942722 3.36E-06 3.35E-06 mr1396 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