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Detailed information for vg0507818456:

Variant ID: vg0507818456 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 7818456
Reference Allele: CAlternative Allele: T,G
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGGTGTTCTCTCTCGAAGGTGAAGCTGAAGTTTCGATATAGAAAACATGAAACCCCATAACTTGAAAAATAGATCTAACTGATATGTTAAAACAACTTCT[C/T,G]
TAAAAAAGATTTTATATGAAATTATCATATAGTATTTGAAAAAAACGTGTTAACGAAAACATAGATAAAATATACTACCTTCGTCCGAAAATATAAGAGA

Reverse complement sequence

TCTCTTATATTTTCGGACGAAGGTAGTATATTTTATCTATGTTTTCGTTAACACGTTTTTTTCAAATACTATATGATAATTTCATATAAAATCTTTTTTA[G/A,C]
AGAAGTTGTTTTAACATATCAGTTAGATCTATTTTTCAAGTTATGGGGTTTCATGTTTTCTATATCGAAACTTCAGCTTCACCTTCGAGAGAGAACACCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.10% 3.90% 0.00% 0.00% G: 0.02%
All Indica  2759 98.40% 1.60% 0.00% 0.00% G: 0.04%
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 50.90% 49.10% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 97.30% 2.70% 0.00% 0.00% NA
Indica Intermediate  786 97.50% 2.40% 0.00% 0.00% G: 0.13%
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0507818456 C -> T LOC_Os05g14010-LOC_Os05g14030 intergenic_region ; MODIFIER silent_mutation Average:62.609; most accessible tissue: Callus, score: 83.55 N N N N
vg0507818456 C -> G LOC_Os05g14010-LOC_Os05g14030 intergenic_region ; MODIFIER silent_mutation Average:62.609; most accessible tissue: Callus, score: 83.55 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0507818456 NA 4.12E-09 mr1348 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
vg0507818456 NA 7.11E-07 mr1126_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
vg0507818456 2.81E-06 NA mr1904_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