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Detailed information for vg1218065288:

Variant ID: vg1218065288 (JBrowse)Variation Type: SNP
Chromosome: chr12Position: 18065288
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: 116. )

Flanking Sequence (100 bp) in Reference Genome:


CCCAGATGATATTCAAATCTAAGTTTAGGGACCGAGGTGACACAACTGAACAAGTTGGAGAATCTAAATGAGTGATCTGCAATTTTAGGGACCGGGATGA[C/T]
ATAGTTGAACAAGTTTGAGGACCTGAACGGTCGATTTGCGAGTTTAGGGACCGCTATGACACAGCGGTACAAGTTTAGGGACAGGTGATGGTCTTTACTC

Reverse complement sequence

GAGTAAAGACCATCACCTGTCCCTAAACTTGTACCGCTGTGTCATAGCGGTCCCTAAACTCGCAAATCGACCGTTCAGGTCCTCAAACTTGTTCAACTAT[G/A]
TCATCCCGGTCCCTAAAATTGCAGATCACTCATTTAGATTCTCCAACTTGTTCAGTTGTGTCACCTCGGTCCCTAAACTTAGATTTGAATATCATCTGGG

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 91.80% 8.20% 0.04% 0.00% NA
All Indica  2759 88.60% 11.30% 0.07% 0.00% NA
All Japonica  1512 95.20% 4.80% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 93.40% 6.60% 0.00% 0.00% NA
Indica II  465 92.70% 7.30% 0.00% 0.00% NA
Indica III  913 86.00% 13.80% 0.22% 0.00% NA
Indica Intermediate  786 85.60% 14.40% 0.00% 0.00% NA
Temperate Japonica  767 99.70% 0.30% 0.00% 0.00% NA
Tropical Japonica  504 96.00% 4.00% 0.00% 0.00% NA
Japonica Intermediate  241 79.30% 20.70% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 96.70% 3.30% 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
vg1218065288 C -> T LOC_Os12g30130.1 upstream_gene_variant ; 3279.0bp to feature; MODIFIER silent_mutation Average:34.054; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N
vg1218065288 C -> T LOC_Os12g30120-LOC_Os12g30130 intergenic_region ; MODIFIER silent_mutation Average:34.054; most accessible tissue: Zhenshan97 panicle, score: 63.607 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1218065288 3.87E-06 3.88E-06 mr1273 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
vg1218065288 6.64E-06 6.64E-06 mr1321 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
vg1218065288 3.63E-06 3.62E-06 mr1340 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
vg1218065288 4.21E-06 4.21E-06 mr1340 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