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Detailed information for vg0412755385:

Variant ID: vg0412755385 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 12755385
Reference Allele: GAlternative Allele: GA,T
Primary Allele: GSecondary Allele: GA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GCCCGCCATTTATGTTTTATGTATTTCCAGAAATTTATTTATGACCTTTCTTAGCCATTAAAAATTGCTGGAAAATTATGGTCAATTATTTGATCACTCA[G/GA,T]
AAAATTATTTCTAGTTAAATGGAACCAACAGGAAGTTTAGCTAGAAAGAAATTAATGATATGATATTATATTTGACCAATGTTAATATGATTTCATGTCA

Reverse complement sequence

TGACATGAAATCATATTAACATTGGTCAAATATAATATCATATCATTAATTTCTTTCTAGCTAAACTTCCTGTTGGTTCCATTTAACTAGAAATAATTTT[C/TC,A]
TGAGTGATCAAATAATTGACCATAATTTTCCAGCAATTTTTAATGGCTAAGAAAGGTCATAAATAAATTTCTGGAAATACATAAAACATAAATGGCGGGC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of GA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 43.40% 0.40% 2.43% 53.58% T: 0.13%
All Indica  2759 16.10% 0.80% 3.66% 79.34% T: 0.18%
All Japonica  1512 96.40% 0.00% 0.53% 3.11% NA
Aus  269 3.30% 0.00% 1.86% 94.42% T: 0.37%
Indica I  595 5.20% 0.20% 2.52% 92.10% NA
Indica II  465 12.90% 3.40% 2.58% 80.86% T: 0.22%
Indica III  913 26.50% 0.10% 4.27% 69.00% T: 0.11%
Indica Intermediate  786 14.00% 0.40% 4.45% 80.79% T: 0.38%
Temperate Japonica  767 98.40% 0.00% 0.26% 1.30% NA
Tropical Japonica  504 93.30% 0.00% 1.19% 5.56% NA
Japonica Intermediate  241 96.30% 0.00% 0.00% 3.73% NA
VI/Aromatic  96 92.70% 0.00% 0.00% 7.29% NA
Intermediate  90 60.00% 0.00% 1.11% 38.89% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0412755385 G -> DEL N N silent_mutation Average:7.02; most accessible tissue: Callus, score: 22.586 N N N N
vg0412755385 G -> GA LOC_Os04g22510.1 upstream_gene_variant ; 4720.0bp to feature; MODIFIER silent_mutation Average:7.02; most accessible tissue: Callus, score: 22.586 N N N N
vg0412755385 G -> GA LOC_Os04g22510-LOC_Os04g22520 intergenic_region ; MODIFIER silent_mutation Average:7.02; most accessible tissue: Callus, score: 22.586 N N N N
vg0412755385 G -> T LOC_Os04g22510.1 upstream_gene_variant ; 4719.0bp to feature; MODIFIER silent_mutation Average:7.02; most accessible tissue: Callus, score: 22.586 N N N N
vg0412755385 G -> T LOC_Os04g22510-LOC_Os04g22520 intergenic_region ; MODIFIER silent_mutation Average:7.02; most accessible tissue: Callus, score: 22.586 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0412755385 NA 2.59E-08 mr1595 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
vg0412755385 NA 4.03E-08 mr1770 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
vg0412755385 1.69E-06 1.69E-06 mr1786 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
vg0412755385 7.82E-07 4.20E-08 mr1910 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
vg0412755385 NA 3.98E-06 mr1955 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