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Detailed information for vg0502440516:

Variant ID: vg0502440516 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2440516
Reference Allele: GAlternative Allele: A
Primary Allele: GSecondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:


AAAATGAGCACATTTTTGGTTCAGCCCAGCATTACTCACTTATCTGACTATTGCTAAGCAGTTTTGGAATATCAAACGCCCAGATGATAATCTTAAAGTG[G/A]
CCAATTTATCTTCTTTTGTAATCAGTTTCGCTACAGCACCTGCTGCTCTAGCTAATTGTTCATCCTTTCCACGTGTGGTTTCTATATTATATATGGCCGT

Reverse complement sequence

ACGGCCATATATAATATAGAAACCACACGTGGAAAGGATGAACAATTAGCTAGAGCAGCAGGTGCTGTAGCGAAACTGATTACAAAAGAAGATAAATTGG[C/T]
CACTTTAAGATTATCATCTGGGCGTTTGATATTCCAAAACTGCTTAGCAATAGTCAGATAAGTGAGTAATGCTGGGCTGAACCAAAAATGTGCTCATTTT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.80% 3.20% 0.00% 0.00% NA
All Indica  2759 95.70% 4.30% 0.00% 0.00% NA
All Japonica  1512 97.90% 2.10% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.50% 0.50% 0.00% 0.00% NA
Indica II  465 96.30% 3.70% 0.00% 0.00% NA
Indica III  913 96.10% 3.90% 0.00% 0.00% NA
Indica Intermediate  786 91.90% 8.10% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 98.80% 1.20% 0.00% 0.00% NA
Japonica Intermediate  241 89.60% 10.40% 0.00% 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
vg0502440516 G -> A LOC_Os05g05020.1 upstream_gene_variant ; 2934.0bp to feature; MODIFIER silent_mutation Average:46.818; most accessible tissue: Callus, score: 80.404 N N N N
vg0502440516 G -> A LOC_Os05g05020-LOC_Os05g05030 intergenic_region ; MODIFIER silent_mutation Average:46.818; most accessible tissue: Callus, score: 80.404 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502440516 8.71E-08 6.47E-07 mr1128 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