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Detailed information for vg0518025487:

Variant ID: vg0518025487 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 18025487
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TTATTTTTTCTTTTTTTTGTTATATGTATAAGGGTAAATTAGACAATTCACCATATATTTTATATATGAATGATGATATGGTATATTCATATGACGATTT[C/T]
GGTAAACGAGCGAAACTTTAAGGATACATTGACTATTCTCCCAAAATGAAAAGTCATGCGCCACGGTTTTACCACCGTACTACTGGTTTCTATTTTTCAG

Reverse complement sequence

CTGAAAAATAGAAACCAGTAGTACGGTGGTAAAACCGTGGCGCATGACTTTTCATTTTGGGAGAATAGTCAATGTATCCTTAAAGTTTCGCTCGTTTACC[G/A]
AAATCGTCATATGAATATACCATATCATCATTCATATATAAAATATATGGTGAATTGTCTAATTTACCCTTATACATATAACAAAAAAAAGAAAAAATAA

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 99.40% 0.40% 0.21% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 98.20% 1.20% 0.60% 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  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 99.90% 0.10% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 96.60% 2.20% 1.17% 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  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 98.90% 0.00% 1.11% 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
vg0518025487 C -> T LOC_Os05g31020-LOC_Os05g31040 intergenic_region ; MODIFIER silent_mutation Average:69.494; most accessible tissue: Callus, score: 89.876 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0518025487 7.53E-08 7.53E-08 mr1855 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
vg0518025487 NA 8.35E-06 mr1008_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
vg0518025487 2.17E-06 2.17E-06 mr1191_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
vg0518025487 NA 2.14E-07 mr1274_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
vg0518025487 2.08E-06 2.07E-06 mr1587_2 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
vg0518025487 NA 7.95E-06 mr1792_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
vg0518025487 NA 2.42E-07 mr1842_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