Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0502188071:

Variant ID: vg0502188071 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 2188071
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:


CACCCTACTAAACTTATTTTTAGGTAGGAGGGAGTAGCGTGCATTCGGTGCGTGCATGTGTGCAGTGGCGGATTTAGGCCATTTCTGTGGGGTCGGCTGA[C/T]
CCCACAGTTTTTTGAAAAACACCCTTTAAATCTCGATTTTCATGTATAATCCAAAAATAATTAGAGAAATGACTCTACTTAAATATAAATCACTAGTAAT

Reverse complement sequence

ATTACTAGTGATTTATATTTAAGTAGAGTCATTTCTCTAATTATTTTTGGATTATACATGAAAATCGAGATTTAAAGGGTGTTTTTCAAAAAACTGTGGG[G/A]
TCAGCCGACCCCACAGAAATGGCCTAAATCCGCCACTGCACACATGCACGCACCGAATGCACGCTACTCCCTCCTACCTAAAAATAAGTTTAGTAGGGTG

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 68.30% 31.50% 0.21% 0.00% NA
All Indica  2759 48.10% 51.50% 0.36% 0.00% NA
All Japonica  1512 97.00% 3.00% 0.00% 0.00% NA
Aus  269 97.40% 2.60% 0.00% 0.00% NA
Indica I  595 29.40% 70.60% 0.00% 0.00% NA
Indica II  465 32.50% 67.10% 0.43% 0.00% NA
Indica III  913 76.30% 23.40% 0.22% 0.00% NA
Indica Intermediate  786 38.70% 60.60% 0.76% 0.00% NA
Temperate Japonica  767 98.60% 1.40% 0.00% 0.00% NA
Tropical Japonica  504 97.60% 2.40% 0.00% 0.00% NA
Japonica Intermediate  241 90.90% 9.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 82.20% 17.80% 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
vg0502188071 C -> T LOC_Os05g04640.1 upstream_gene_variant ; 3131.0bp to feature; MODIFIER silent_mutation Average:44.847; most accessible tissue: Callus, score: 73.918 N N N N
vg0502188071 C -> T LOC_Os05g04640-LOC_Os05g04650 intergenic_region ; MODIFIER silent_mutation Average:44.847; most accessible tissue: Callus, score: 73.918 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0502188071 NA 3.73E-06 mr1189 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
vg0502188071 NA 1.16E-06 mr1782 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
vg0502188071 NA 2.43E-16 mr1807 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
vg0502188071 1.98E-06 NA mr1952_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
vg0502188071 3.75E-07 2.49E-09 mr1952_2 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