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Detailed information for vg1120137948:

Variant ID: vg1120137948 (JBrowse)Variation Type: SNP
Chromosome: chr11Position: 20137948
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: 368. )

Flanking Sequence (100 bp) in Reference Genome:


TGAAGTTAGAAGATGAGGTAGTTCGCATTACCAAGACAGGCATGTACAACTTGTTCTTCATTTCCTGTGATCCAAAACTGAGAGGCCTTAGTATGAGTGG[G/T]
AAGACAGTCTGGAGGAATCCTGGCGGCTACCTACCAGGGCGGATGGCACCTTTGATGAAATTTTACGTTTTTATGTCACTGGCTTATCTATTGGTCATGG

Reverse complement sequence

CCATGACCAATAGATAAGCCAGTGACATAAAAACGTAAAATTTCATCAAAGGTGCCATCCGCCCTGGTAGGTAGCCGCCAGGATTCCTCCAGACTGTCTT[C/A]
CCACTCATACTAAGGCCTCTCAGTTTTGGATCACAGGAAATGAAGAACAAGTTGTACATGCCTGTCTTGGTAATGCGAACTACCTCATCTTCTAACTTCA

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 99.00% 0.70% 0.30% 0.00% NA
All Indica  2759 100.00% 0.00% 0.04% 0.00% NA
All Japonica  1512 97.00% 2.10% 0.86% 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 99.80% 0.00% 0.22% 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 94.80% 3.50% 1.69% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 97.90% 2.10% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 100.00% 0.00% 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
vg1120137948 G -> T LOC_Os11g34360.1 synonymous_variant ; p.Gly195Gly; LOW synonymous_codon Average:77.625; most accessible tissue: Zhenshan97 young leaf, score: 88.387 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg1120137948 NA 1.80E-08 Awn_length Jap_All Not Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection, Proc Natl Acad Sci USA, 112(39): E5411-E5419, PMID:26358652
vg1120137948 NA 6.56E-08 mr1757 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
vg1120137948 NA 6.67E-11 mr1549_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
vg1120137948 NA 7.19E-12 mr1757_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