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Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg1116343038:

Variant ID: vg1116343038 (JBrowse)Variation Type: INDEL
Chromosome: chr11Position: 16343038
Reference Allele: TAlternative Allele: A,TGTTGGGATACGCGTA,TGTTG,TGTTGGGATATGCGTA,TCACTAACACTATAA
Primary Allele: TSecondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTTTCTCTACACTAACTTTTAGGTAATGCTATTTCTTTCTACTCTCACGAAGCTAGCTACATCACCTTATTGTTTTAGTCTTTGGATCATTCATCTATA[T/A,TGTTGGGATACGCGTA,TGTTG,TGTTGGGATATGCGTA,TCACTAACACTATAA]
GGCATAGATCGTTTCGTTCTACTTATCTCATGGAGCCATGTGTATCATCTCGTCAACCATTTTTTTACCACATGAAAACCATGATCTTCATTTTTGGCCT

Reverse complement sequence

AGGCCAAAAATGAAGATCATGGTTTTCATGTGGTAAAAAAATGGTTGACGAGATGATACACATGGCTCCATGAGATAAGTAGAACGAAACGATCTATGCC[A/T,TACGCGTATCCCAACA,CAACA,TACGCATATCCCAACA,TTATAGTGTTAGTGA]
TATAGATGAATGATCCAAAGACTAAAACAATAAGGTGATGTAGCTAGCTTCGTGAGAGTAGAAAGAAATAGCATTACCTAAAAGTTAGTGTAGAGAAACT

Allele Frequencies:

Populations Population SizeFrequency of T(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 63.80% 4.90% 29.67% 0.74% TGTTGGGATACGCGTA: 0.40%; TGTTGGGATATGCGTA: 0.30%; TGTTG: 0.19%
All Indica  2759 57.80% 6.70% 34.00% 0.40% TGTTGGGATATGCGTA: 0.51%; TGTTGGGATACGCGTA: 0.29%; TGTTG: 0.22%
All Japonica  1512 74.90% 1.80% 21.10% 1.52% TGTTGGGATACGCGTA: 0.53%; TGTTG: 0.20%
Aus  269 49.80% 5.60% 43.12% 0.37% TGTTGGGATACGCGTA: 1.12%
Indica I  595 57.60% 2.90% 37.65% 0.67% TGTTGGGATATGCGTA: 0.67%; TGTTGGGATACGCGTA: 0.34%; TGTTG: 0.17%
Indica II  465 57.00% 7.10% 34.84% 0.43% TGTTGGGATATGCGTA: 0.43%; TGTTG: 0.22%
Indica III  913 60.00% 10.10% 28.70% 0.22% TGTTGGGATATGCGTA: 0.55%; TGTTGGGATACGCGTA: 0.33%; TGTTG: 0.11%
Indica Intermediate  786 56.00% 5.60% 36.90% 0.38% TGTTG: 0.38%; TGTTGGGATATGCGTA: 0.38%; TGTTGGGATACGCGTA: 0.38%
Temperate Japonica  767 89.60% 0.70% 9.65% 0.13% NA
Tropical Japonica  504 61.30% 3.00% 30.56% 3.37% TGTTGGGATACGCGTA: 1.39%; TGTTG: 0.40%
Japonica Intermediate  241 56.40% 2.90% 37.76% 2.07% TGTTGGGATACGCGTA: 0.41%; TGTTG: 0.41%
VI/Aromatic  96 99.00% 0.00% 1.04% 0.00% NA
Intermediate  90 64.40% 4.40% 31.11% 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
vg1116343038 T -> A LOC_Os11g28380.1 upstream_gene_variant ; 2456.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> A LOC_Os11g28400.1 upstream_gene_variant ; 874.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> A LOC_Os11g28370.1 downstream_gene_variant ; 4499.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> A LOC_Os11g28390.1 downstream_gene_variant ; 259.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> A LOC_Os11g28390-LOC_Os11g28400 intergenic_region ; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATATGCGTA LOC_Os11g28380.1 upstream_gene_variant ; 2457.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATATGCGTA LOC_Os11g28400.1 upstream_gene_variant ; 873.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATATGCGTA LOC_Os11g28370.1 downstream_gene_variant ; 4500.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATATGCGTA LOC_Os11g28390.1 downstream_gene_variant ; 260.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATATGCGTA LOC_Os11g28390-LOC_Os11g28400 intergenic_region ; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> DEL N N silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATACGCGTA LOC_Os11g28380.1 upstream_gene_variant ; 2457.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATACGCGTA LOC_Os11g28400.1 upstream_gene_variant ; 873.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATACGCGTA LOC_Os11g28370.1 downstream_gene_variant ; 4500.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATACGCGTA LOC_Os11g28390.1 downstream_gene_variant ; 260.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTGGGATACGCGTA LOC_Os11g28390-LOC_Os11g28400 intergenic_region ; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTG LOC_Os11g28380.1 upstream_gene_variant ; 2457.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTG LOC_Os11g28400.1 upstream_gene_variant ; 873.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTG LOC_Os11g28370.1 downstream_gene_variant ; 4500.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTG LOC_Os11g28390.1 downstream_gene_variant ; 260.0bp to feature; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TGTTG LOC_Os11g28390-LOC_Os11g28400 intergenic_region ; MODIFIER silent_mutation Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TCACTAACACTATAA LOC_Os11g28380.1 upstream_gene_variant ; 2457.0bp to feature; MODIFIER N Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TCACTAACACTATAA LOC_Os11g28400.1 upstream_gene_variant ; 873.0bp to feature; MODIFIER N Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TCACTAACACTATAA LOC_Os11g28370.1 downstream_gene_variant ; 4500.0bp to feature; MODIFIER N Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TCACTAACACTATAA LOC_Os11g28390.1 downstream_gene_variant ; 260.0bp to feature; MODIFIER N Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N
vg1116343038 T -> TCACTAACACTATAA LOC_Os11g28390-LOC_Os11g28400 intergenic_region ; MODIFIER N Average:46.539; most accessible tissue: Callus, score: 91.349 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1116343038 1.31E-06 NA mr1410 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