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Detailed information for vg0218969543:

Variant ID: vg0218969543 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 18969543
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: 313. )

Flanking Sequence (100 bp) in Reference Genome:


GAACATTGCCACCACTTGTGGTAGCAGCAGCAGCAGCAGCATCGGACGCCTCCTTGGCGACCTTCTCCTTCAGTGACGCCACCACCTGATGGTCAGCGAG[C/T]
GGCCCGATGATGTCAGTCAGAGGAAGAGCCTACGCTTAATCAAGTCACAAAGCGATCTCGGAAGAAAAACGCAGAATGCCTATTGAGTACACTTACATTG

Reverse complement sequence

CAATGTAAGTGTACTCAATAGGCATTCTGCGTTTTTCTTCCGAGATCGCTTTGTGACTTGATTAAGCGTAGGCTCTTCCTCTGACTGACATCATCGGGCC[G/A]
CTCGCTGACCATCAGGTGGTGGCGTCACTGAAGGAGAAGGTCGCCAAGGAGGCGTCCGATGCTGCTGCTGCTGCTGCTACCACAAGTGGTGGCAATGTTC

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 95.80% 3.90% 0.23% 0.00% NA
All Indica  2759 93.00% 6.60% 0.40% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 99.80% 0.00% 0.17% 0.00% NA
Indica II  465 78.50% 20.00% 1.51% 0.00% NA
Indica III  913 95.30% 4.70% 0.00% 0.00% NA
Indica Intermediate  786 93.80% 5.90% 0.38% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0218969543 C -> T LOC_Os02g32100.1 synonymous_variant ; p.Pro227Pro; LOW synonymous_codon Average:53.05; most accessible tissue: Zhenshan97 flag leaf, score: 72.012 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0218969543 NA 4.35E-06 mr1130 Ind_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
vg0218969543 NA 2.54E-06 mr1148 Ind_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
vg0218969543 NA 1.84E-09 mr1855 Ind_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
vg0218969543 NA 1.41E-08 mr1931 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
vg0218969543 NA 3.91E-07 mr1855_2 Ind_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