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Detailed information for vg0517184431:

Variant ID: vg0517184431 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 17184431
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


GACAAATTACATTATAATTACATGCAAATTACAATATAGTTACACTAAAATTAGGGGTGATCAGAATCGGTCGGAATCGGTTGCATATCTTTGAATGCGA[C/T]
GCTCAATCGGTCAATAATTGACTGTATTTGTCACTTAAACTACTCAGTGTCGATATTAATATGATGCAGGAAGAATTAGAAAAAACTAAATTTATATATA

Reverse complement sequence

TATATATAAATTTAGTTTTTTCTAATTCTTCCTGCATCATATTAATATCGACACTGAGTAGTTTAAGTGACAAATACAGTCAATTATTGACCGATTGAGC[G/A]
TCGCATTCAAAGATATGCAACCGATTCCGACCGATTCTGATCACCCCTAATTTTAGTGTAACTATATTGTAATTTGCATGTAATTATAATGTAATTTGTC

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 98.50% 1.20% 0.36% 0.00% NA
All Indica  2759 99.90% 0.10% 0.00% 0.00% NA
All Japonica  1512 95.40% 3.50% 1.12% 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 99.60% 0.40% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 92.40% 5.60% 1.96% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 95.90% 3.30% 0.83% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 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
vg0517184431 C -> T LOC_Os05g29720.1 downstream_gene_variant ; 1281.0bp to feature; MODIFIER silent_mutation Average:41.4; most accessible tissue: Callus, score: 67.549 N N N N
vg0517184431 C -> T LOC_Os05g29710-LOC_Os05g29720 intergenic_region ; MODIFIER silent_mutation Average:41.4; most accessible tissue: Callus, score: 67.549 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0517184431 2.89E-07 2.89E-07 mr1456 Jap_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