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Detailed information for vg0214541889:

Variant ID: vg0214541889 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 14541889
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:


TGCATGAAATTACCACCTCCTTTTTAAATATATAACGTTGTTGATTTTTGGACGTGACGTTTGACCATTTGTTTAATCTAAAAATTATGTAAATTTAAGT[C/A]
ATGCTTAAAAGTCCTTCTAAGCATGACTTATATTTATATCTTTGCGTATTCATACTAAAATTTTGAATTAGACAAATATTCAAATGTCCAAAAGCCAACA

Reverse complement sequence

TGTTGGCTTTTGGACATTTGAATATTTGTCTAATTCAAAATTTTAGTATGAATACGCAAAGATATAAATATAAGTCATGCTTAGAAGGACTTTTAAGCAT[G/T]
ACTTAAATTTACATAATTTTTAGATTAAACAAATGGTCAAACGTCACGTCCAAAAATCAACAACGTTATATATTTAAAAAGGAGGTGGTAATTTCATGCA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 96.70% 3.00% 0.34% 0.00% NA
All Indica  2759 100.00% 0.00% 0.00% 0.00% NA
All Japonica  1512 89.90% 9.10% 1.06% 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  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 100.00% 0.00% 0.00% 0.00% NA
Temperate Japonica  767 97.00% 2.90% 0.13% 0.00% NA
Tropical Japonica  504 81.30% 16.30% 2.38% 0.00% NA
Japonica Intermediate  241 85.10% 13.70% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 94.40% 5.60% 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
vg0214541889 C -> A LOC_Os02g25060.1 upstream_gene_variant ; 4341.0bp to feature; MODIFIER silent_mutation Average:23.308; most accessible tissue: Zhenshan97 root, score: 36.298 N N N N
vg0214541889 C -> A LOC_Os02g25060.2 upstream_gene_variant ; 4386.0bp to feature; MODIFIER silent_mutation Average:23.308; most accessible tissue: Zhenshan97 root, score: 36.298 N N N N
vg0214541889 C -> A LOC_Os02g25060-LOC_Os02g25070 intergenic_region ; MODIFIER silent_mutation Average:23.308; most accessible tissue: Zhenshan97 root, score: 36.298 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0214541889 NA 8.93E-06 mr1510_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
vg0214541889 NA 3.00E-10 mr1676_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
vg0214541889 4.90E-06 NA mr1742_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
vg0214541889 8.79E-07 NA mr1871_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