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Detailed information for vg1118281157:

Variant ID: vg1118281157 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 18281157
Reference Allele: GAlternative Allele: T
Primary Allele: GSecondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


ACACTTGGGAACTGCTCCAACGTCCTTCATCTAACGCTGTTGTGACGGATCGGAGATTATGGTTCAGATTTATGATTGTGACAAAACTCACTATATTTCC[G/T]
CTTGGTCAGACCCCAAAGATGCAGATTTTCTAAGTAGAAATGTGATAAATTGTGTGGGACATTATATATAGTAGAAATGTGATAAATTCTGATCCGCTGG

Reverse complement sequence

CCAGCGGATCAGAATTTATCACATTTCTACTATATATAATGTCCCACACAATTTATCACATTTCTACTTAGAAAATCTGCATCTTTGGGGTCTGACCAAG[C/A]
GGAAATATAGTGAGTTTTGTCACAATCATAAATCTGAACCATAATCTCCGATCCGTCACAACAGCGTTAGATGAAGGACGTTGGAGCAGTTCCCAAGTGT

Allele Frequencies:

Populations Population SizeFrequency of G(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 90.90% 9.10% 0.00% 0.00% NA
All Indica  2759 99.70% 0.30% 0.00% 0.00% NA
All Japonica  1512 75.70% 24.30% 0.00% 0.00% NA
Aus  269 86.20% 13.80% 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 99.20% 0.80% 0.00% 0.00% NA
Temperate Japonica  767 97.70% 2.30% 0.00% 0.00% NA
Tropical Japonica  504 42.50% 57.50% 0.00% 0.00% NA
Japonica Intermediate  241 75.10% 24.90% 0.00% 0.00% NA
VI/Aromatic  96 95.80% 4.20% 0.00% 0.00% NA
Intermediate  90 85.60% 14.40% 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
vg1118281157 G -> T LOC_Os11g31320-LOC_Os11g31330 intergenic_region ; MODIFIER silent_mutation Average:47.556; most accessible tissue: Zhenshan97 young leaf, score: 76.099 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1118281157 3.59E-07 NA mr1241 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
vg1118281157 NA 2.31E-11 mr1241 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
vg1118281157 NA 7.74E-06 mr1194_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
vg1118281157 NA 4.01E-06 mr1730_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