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Detailed information for vg0514922521:

Variant ID: vg0514922521 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 14922521
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TCAGCTGTCACGTAGACTAAAACCAGGATCAAAATTGCTGAAGGATCTCGGGTGACCGGTTTTGTATAGTTGAGGGACCCCACATATCTGGTTTTGCGGT[C/T]
GGAGCACGTTTTTGAATCCCGCTGATAAGTTAAGGGACCTTCGGTGCACTTTTTCCCAAGAATATTGGGCATGCAGGCCGAATCCGCATATACGCCTAAG

Reverse complement sequence

CTTAGGCGTATATGCGGATTCGGCCTGCATGCCCAATATTCTTGGGAAAAAGTGCACCGAAGGTCCCTTAACTTATCAGCGGGATTCAAAAACGTGCTCC[G/A]
ACCGCAAAACCAGATATGTGGGGTCCCTCAACTATACAAAACCGGTCACCCGAGATCCTTCAGCAATTTTGATCCTGGTTTTAGTCTACGTGACAGCTGA

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 97.10% 2.90% 0.00% 0.00% NA
All Indica  2759 99.60% 0.40% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 54.60% 45.40% 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 99.00% 1.00% 0.00% 0.00% NA
Indica Intermediate  786 99.60% 0.40% 0.00% 0.00% NA
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  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 99.00% 1.00% 0.00% 0.00% NA
Intermediate  90 98.90% 1.10% 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
vg0514922521 C -> T LOC_Os05g25660.1 downstream_gene_variant ; 380.0bp to feature; MODIFIER silent_mutation Average:68.578; most accessible tissue: Zhenshan97 young leaf, score: 84.035 N N N N
vg0514922521 C -> T LOC_Os05g25660-LOC_Os05g25670 intergenic_region ; MODIFIER silent_mutation Average:68.578; most accessible tissue: Zhenshan97 young leaf, score: 84.035 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0514922521 NA 7.29E-16 mr1158 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
vg0514922521 NA 4.34E-07 mr1343 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
vg0514922521 NA 3.48E-14 mr1496 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
vg0514922521 NA 9.72E-11 mr1608 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
vg0514922521 3.20E-08 NA mr1550_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