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Detailed information for vg0525416226:

Variant ID: vg0525416226 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 25416226
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GTGCTAGCTCGGGGCGTGACACGGTGGCAGGAGGACGGTGCCAGAGAGGCTGGCGCCGTCCCGTTGGATGACGGCGCCAGCCACTCTGGCGCCCCAAAAA[G/T]
AACTATTTCTGGGATAAGTTTTTTCAGAGGTCTATTTGCGAAATAAGTTTTTTAAAAGGACAAAAATGTGAAAAATCCAGATGTTTATTACTACTCCGTA

Reverse complement sequence

TACGGAGTAGTAATAAACATCTGGATTTTTCACATTTTTGTCCTTTTAAAAAACTTATTTCGCAAATAGACCTCTGAAAAAACTTATCCCAGAAATAGTT[C/A]
TTTTTGGGGCGCCAGAGTGGCTGGCGCCGTCATCCAACGGGACGGCGCCAGCCTCTCTGGCACCGTCCTCCTGCCACCGTGTCACGCCCCGAGCTAGCAC

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 92.40% 6.60% 1.04% 0.00% NA
All Indica  2759 98.20% 0.10% 1.67% 0.00% NA
All Japonica  1512 79.90% 19.90% 0.20% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 97.60% 0.60% 1.72% 0.00% NA
Indica III  913 97.00% 0.00% 2.96% 0.00% NA
Indica Intermediate  786 98.60% 0.00% 1.40% 0.00% NA
Temperate Japonica  767 86.20% 13.60% 0.26% 0.00% NA
Tropical Japonica  504 80.80% 19.00% 0.20% 0.00% NA
Japonica Intermediate  241 58.10% 41.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 0.00% 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
vg0525416226 G -> T LOC_Os05g43720.1 upstream_gene_variant ; 2983.0bp to feature; MODIFIER silent_mutation Average:50.497; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0525416226 G -> T LOC_Os05g43730.1 upstream_gene_variant ; 1511.0bp to feature; MODIFIER silent_mutation Average:50.497; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N
vg0525416226 G -> T LOC_Os05g43720-LOC_Os05g43730 intergenic_region ; MODIFIER silent_mutation Average:50.497; most accessible tissue: Minghui63 panicle, score: 70.194 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0525416226 NA 1.06E-06 mr1280 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
vg0525416226 NA 2.80E-07 mr1280 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
vg0525416226 NA 2.18E-08 mr1807 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
vg0525416226 NA 7.34E-06 mr1164_2 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
vg0525416226 1.04E-07 NA mr1842_2 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
vg0525416226 6.37E-06 7.98E-10 mr1947_2 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